Evolutionary classification of protein domain structures

alpha arraysalpha-helix arrays with mainly perpendicular helices

alpha bundlesalpha-helix bundles with mainly parallel helices

alpha superhelicesrepeating alpha-helix hairpins form a superhelix

alpha duplicates or obligate multimersalpha duplicates or monomers associate together to form a compact domain

alpha complex topologyalpha domain with complex and unique topology that cannot be described as array or bundle or superhelix

beta barrelssingle beta-sheet folded upon itself to form a barrel

X: cradle loop barrel

Refs: Structure 14, 1489-1498; Current opinion in structural biology 18, 358-365

X: N-terminal domain of TAP-binding protein-related

X: P22 coat protein insertion domain

X: Catalytic domain of hepatitis C virus NS2-3 protease

X: N-terminal domain of minor coat protein pIII

X: uncharacterized protein RUMGNA_01417

X: Ribosomal protein L21p

X: Ribosomal protein L25-like

X: Uncharacterized protein from gene locus rrnAC0354

X: Replication foci-targeting sequence N-terminal domain

X: Protein CLP1 C-terminal domain

X: Glycoside hydrolase family 127 C-terminal domain

X: EV matrix protein

X: LigT-like

X: Urease metallochperone UreE-N

X: Target recognition domain of zoocin A

X: Polymyxin B resistance protein

X: Cuben fold of PcncAAAD

X: OB-fold

X: GroES-like

X: Uncharacterized protein Dsy0195

X: SH3

X: IL8-related

X: UL131A-like

X: UL128 C-terminal domain

X: Cell division protein ZapC N-terminal domain

X: hypothetical protein TTMA177

X: Hantavirus structural glycoprotein Gn ectodomain subdomain III

X: MutM N-terminal domain-like

X: Ribosomal protein L14-like

X: YopX, C-terminal domain-like

X: VC0467-like

X: MMP1218-like

X: MFPT repeat

X: Barrel domain in upper collar protein

X: barrel domain in putative modulator of DNA gyrase, PmbA/TldD

X: beta-barrel domain in acetyl-CoA synthetase-like proteins

X: FimD N-terminal domain-like

X: Micronemal adhesive repeat

X: Coronavirus NSP8-like

X: PDZ domain

H: PDZ domain

T: PDZ domain

F: PDZ_5

F: PDZ_3

F: PDZ,PDZ_5

F: PDZ_2

F: PDZ,EBP50_C

F: GRASP55_65

F: Tricorn_PDZ

F: PDZ

Representatives:

e1r6jA1[A:192-273] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Syntenin 1 ; ligands: CL ; X-RAY DIFFRACTION 0.73Å

e2h3lA1[A:1310-1412] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

LAP2 protein ; X-RAY DIFFRACTION 1.000Å

e2fe5A1[A:223-314] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

PRESYNAPTIC PROTEIN SAP102 ; ligands: GOL,SO4 ; X-RAY DIFFRACTION 1.1Å

e1qauA1[A:14-125] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

NEURONAL NITRIC OXIDE SYNTHASE (RESIDUES 1-130) ; X-RAY DIFFRACTION 1.25Å

e1g9oA1[A:9-99] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

NHE-RF ; X-RAY DIFFRACTION 1.5Å

e1n7eA1[A:667-761] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

AMPA receptor interacting protein GRIP ; X-RAY DIFFRACTION 1.5Å

e1tp5A1[A:302-403] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

Presynaptic density protein 95 ; X-RAY DIFFRACTION 1.54Å

e1w9eA2[A:110-194] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

SYNTENIN 1 ; X-RAY DIFFRACTION 1.560Å

e5f67A1[A:351-448] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Inactivation-no-after-potential D protein ; X-RAY DIFFRACTION 1.76Å

e1ihjA1[A:12-105] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

INAD ; X-RAY DIFFRACTION 1.8Å

e1q3oA1[A:584-687] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Shank1 ; ligands: BR ; X-RAY DIFFRACTION 1.8Å

e2f0aA1[A:251-342] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

Segment polarity protein dishevelled homolog DVL-2 ; ligands: SO4 ; X-RAY DIFFRACTION 1.8Å

e1qavA1[A:75-164] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

ALPHA-1 SYNTROPHIN (RESIDUES 77-171) ; X-RAY DIFFRACTION 1.9Å

e5v6bA2[A:128-218] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PDZ domain-containing protein GIPC1 ; X-RAY DIFFRACTION 1.9Å

e1kwaA1[A:487-574] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

HCASK/LIN-2 PROTEIN ; ligands: SO4 ; X-RAY DIFFRACTION 1.93Å

e2awxB1[B:317-405] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Synapse associated protein 97 ; ligands: HIS ; X-RAY DIFFRACTION 1.80Å

e2iwoB1[B:1822-1927] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

MULTIPLE PDZ DOMAIN PROTEIN ; X-RAY DIFFRACTION 1.7Å

e2iwpA1[A:1832-1927] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

MULTIPLE PDZ DOMAIN PROTEIN ; X-RAY DIFFRACTION 2.15Å

e2fn5A1[A:1-94] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Neurabin-1 ; SOLUTION NMR

e2o2tB1[B:121-231] Image Pymol Jmol Links: PDB, SCOP, CATH

MULTIPLE PDZ DOMAIN PROTEIN ; X-RAY DIFFRACTION 2.7Å

e2jikA1[A:-1-104] Image Pymol Jmol Links: PDB, SCOP, CATH

SYNAPTOJANIN-2 BINDING PROTEIN ; X-RAY DIFFRACTION 1.35Å

e2jikB1[B:-1-104] Image Pymol Jmol Links: PDB, SCOP, CATH

SYNAPTOJANIN-2 BINDING PROTEIN ; X-RAY DIFFRACTION 1.35Å

e2jinA1[A:-1-103] Image Pymol Jmol Links: PDB, SCOP, CATH

SYNAPTOJANIN-2 BINDING PROTEIN ; ligands: NA,SO4 ; X-RAY DIFFRACTION 1.5Å

e2i0lA1[A:318-400] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Disks large homolog 1 ; X-RAY DIFFRACTION 2.3Å

e2i0lB1[B:318-400] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Disks large homolog 1 ; X-RAY DIFFRACTION 2.3Å

e2qt5B2[B:47-135] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Glutamate receptor-interacting protein 1 ; ligands: EDO ; X-RAY DIFFRACTION 2.300Å

e2qt5A2[A:47-135] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Glutamate receptor-interacting protein 1 ; ligands: ACY,EDO ; X-RAY DIFFRACTION 2.300Å

e2egkD1[D:98-194] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

General receptor for phosphoinositides 1-associated scaffold protein ; ligands: PO4 ; X-RAY DIFFRACTION 2.85Å

e2w4fA1[A:725-819] Image Pymol Jmol Links: PDB, SCOP, CATH

PROTEIN LAP4 ; ligands: EDO ; X-RAY DIFFRACTION 1.30Å

e2oqsA1[A:1-92] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Disks large homolog 1 ; SOLUTION NMR

e3ggeB1[B:113-204] Image Pymol Jmol Links: PDB, SCOP, CATH

PDZ domain-containing protein GIPC2 ; ligands: GOL,SO4 ; X-RAY DIFFRACTION 2.60Å

e2vphA1[A:513-610] Image Pymol Jmol Links: PDB, SCOP, CATH

TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 4 ; X-RAY DIFFRACTION 1.90Å

e3cbxA1[A:260-364] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Dishevelled-2 ; ligands: CL,MPD ; X-RAY DIFFRACTION 1.700Å

e3cbxB1[B:261-364] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Dishevelled-2 ; ligands: MPD ; X-RAY DIFFRACTION 1.700Å

e3cbyB1[B:264-367] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Dishevelled-2 ; ligands: EDO ; X-RAY DIFFRACTION 1.500Å

e3cbzA1[A:263-367] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Dishevelled-2 ; ligands: EDO,PO4 ; X-RAY DIFFRACTION 1.380Å

e3cc0A1[A:262-367] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Dishevelled-2 ; X-RAY DIFFRACTION 1.750Å

e3dj1A1[A:9-123] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

TAX1-BINDING PROTEIN 3 ; ligands: SO4 ; X-RAY DIFFRACTION 1.8Å

e2egoA1[A:95-189] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

General receptor for phosphoinositides 1-associated scaffold protein ; X-RAY DIFFRACTION 1.8Å

e2egnA1[A:96-189] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

General receptor for phosphoinositides 1-associated scaffold protein ; X-RAY DIFFRACTION 2.1Å

e2vspB1[B:376-455] Image Pymol Jmol Links: PDB, SCOP, CATH

PDZ DOMAIN-CONTAINING PROTEIN 1 ; X-RAY DIFFRACTION 2.60Å

e2vspC1[C:374-456] Image Pymol Jmol Links: PDB, SCOP, CATH

PDZ DOMAIN-CONTAINING PROTEIN 1 ; X-RAY DIFFRACTION 2.60Å

e2vspD1[D:374-456] Image Pymol Jmol Links: PDB, SCOP, CATH

PDZ DOMAIN-CONTAINING PROTEIN 1 ; X-RAY DIFFRACTION 2.60Å

e3dj3B1[B:12-112] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

TAX1-BINDING PROTEIN 3 ; X-RAY DIFFRACTION 2.4Å

e3diwA1[A:8-115] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

TAX1-BINDING PROTEIN 3 ; X-RAY DIFFRACTION 2.1Å

e3diwB1[B:11-116] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

TAX1-BINDING PROTEIN 3 ; X-RAY DIFFRACTION 2.1Å

e3dj3A1[A:12-111] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

TAX1-BINDING PROTEIN 3 ; X-RAY DIFFRACTION 2.4Å

e3dj3C1[C:12-111] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

TAX1-BINDING PROTEIN 3 ; X-RAY DIFFRACTION 2.4Å

e3dj3D1[D:13-111] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

TAX1-BINDING PROTEIN 3 ; X-RAY DIFFRACTION 2.4Å

e2r4hB1[B:2-90] Image Pymol Jmol Links: PDB, SCOP, CATH

Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1 ; X-RAY DIFFRACTION 2.05Å

e2r4hC1[C:-7-90] Image Pymol Jmol Links: PDB, SCOP, CATH

Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1 ; ligands: HIS ; X-RAY DIFFRACTION 2.05Å

e2i04B1[B:450-534] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

MEMBRANE-ASSOCIATED GUANYLATE KINASE, WW AND PDZ DOMAIN-CONTAINING PROTEIN 1 ; ligands: SO4 ; X-RAY DIFFRACTION 2.15Å

e3b76B1[B:401-502] Image Pymol Jmol Links: PDB, SCOP, CATH

E3 ubiquitin-protein ligase LNX ; ligands: EDO ; X-RAY DIFFRACTION 1.75Å

e2pkuA1[A:18-104] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PRKCA-binding protein ; SOLUTION NMR

e3cc0B1[B:260-367] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Dishevelled-2 ; X-RAY DIFFRACTION 1.750Å

e3cc0C1[C:264-367] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Dishevelled-2 ; X-RAY DIFFRACTION 1.750Å

e2k20A1[A:7-110] Image Pymol Jmol Links: PDB, SCOP, CATH

Partitioning-defective 3 homolog ; SOLUTION NMR

e2opgB1[B:1623-1720] Image Pymol Jmol Links: PDB, SCOP, CATH

Multiple PDZ domain protein ; X-RAY DIFFRACTION 1.5Å

e2qt5B1[B:136-239] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Glutamate receptor-interacting protein 1 ; ligands: EDO ; X-RAY DIFFRACTION 2.300Å

e2v90B1[B:245-339] Image Pymol Jmol Links: PDB, SCOP, CATH

PDZ DOMAIN-CONTAINING PROTEIN 3 ; ligands: SO4 ; X-RAY DIFFRACTION 2.00Å

e2v90C1[C:247-339] Image Pymol Jmol Links: PDB, SCOP, CATH

PDZ DOMAIN-CONTAINING PROTEIN 3 ; X-RAY DIFFRACTION 2.00Å

e2v90D1[D:247-339] Image Pymol Jmol Links: PDB, SCOP, CATH

PDZ DOMAIN-CONTAINING PROTEIN 3 ; X-RAY DIFFRACTION 2.00Å

e2v90E1[E:245-339] Image Pymol Jmol Links: PDB, SCOP, CATH

PDZ DOMAIN-CONTAINING PROTEIN 3 ; X-RAY DIFFRACTION 2.00Å

e2v90F1[F:245-339] Image Pymol Jmol Links: PDB, SCOP, CATH

PDZ DOMAIN-CONTAINING PROTEIN 3 ; X-RAY DIFFRACTION 2.00Å

e2egkC1[C:98-194] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

General receptor for phosphoinositides 1-associated scaffold protein ; ligands: PO4 ; X-RAY DIFFRACTION 2.85Å

e2egoB1[B:95-189] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

General receptor for phosphoinositides 1-associated scaffold protein ; X-RAY DIFFRACTION 1.8Å

e2egkB1[B:97-194] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

General receptor for phosphoinositides 1-associated scaffold protein ; ligands: PO4 ; X-RAY DIFFRACTION 2.85Å

e2pntA1[A:97-192] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

General receptor for phosphoinositides 1-associated scaffold protein ; ligands: CL ; X-RAY DIFFRACTION 2.148Å

e2pntB1[B:98-192] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

General receptor for phosphoinositides 1-associated scaffold protein ; X-RAY DIFFRACTION 2.148Å

e2z17A1[A:11-104] Image Pymol Jmol Links: PDB, SCOP, CATH

Pleckstrin homology Sec7 and coiled-coil domains-binding protein ; X-RAY DIFFRACTION 2.5Å

e3dj1B1[B:10-123] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

TAX1-BINDING PROTEIN 3 ; X-RAY DIFFRACTION 1.8Å

e2v1wA1[A:1-89] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PDZ AND LIM DOMAIN PROTEIN 4 ; ligands: EDO ; X-RAY DIFFRACTION 1.900Å

e2v1wB1[B:0-89] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PDZ AND LIM DOMAIN PROTEIN 4 ; ligands: 1PE,EDO,MG ; X-RAY DIFFRACTION 1.900Å

e2uzcB1[B:2-87] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PDZ AND LIM DOMAIN 5 ; ligands: CL,EDO ; X-RAY DIFFRACTION 1.500Å

e2uzcC1[C:0-87] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PDZ AND LIM DOMAIN 5 ; ligands: CL ; X-RAY DIFFRACTION 1.500Å

e2uzcD1[D:0-87] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PDZ AND LIM DOMAIN 5 ; ligands: CL,EDO ; X-RAY DIFFRACTION 1.500Å

e2uzcE1[E:1-87] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PDZ AND LIM DOMAIN 5 ; ligands: CL ; X-RAY DIFFRACTION 1.500Å

e2q3gB1[B:1-88] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PDZ and LIM domain protein 7 ; ligands: CL,EDO ; X-RAY DIFFRACTION 1.11Å

e2qktA1[A:580-664] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

INACTIVATION-NO-AFTER-POTENTIAL D PROTEIN ; X-RAY DIFFRACTION 2.05Å

e2qktB1[B:580-664] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

INACTIVATION-NO-AFTER-POTENTIAL D PROTEIN ; X-RAY DIFFRACTION 2.05Å

e2qkuA1[A:580-664] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

INACTIVATION-NO-AFTER-POTENTIAL D PROTEIN ; X-RAY DIFFRACTION 2.2Å

e2qkuB1[B:580-663] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

INACTIVATION-NO-AFTER-POTENTIAL D PROTEIN ; ligands: GOL ; X-RAY DIFFRACTION 2.2Å

e2qkuC1[C:580-669] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

INACTIVATION-NO-AFTER-POTENTIAL D PROTEIN ; ligands: GOL ; X-RAY DIFFRACTION 2.2Å

e2qkvB1[B:574-665] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Inactivation-no-after-potential D protein ; X-RAY DIFFRACTION 1.55Å

e2yubA1[A:1-118] Image Pymol Jmol Links: PDB, SCOP, CATH

LIM domain kinase 2 ; SOLUTION NMR

e2osgB1[B:84-166] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Tight junction protein ZO-2 ; SOLUTION NMR

e2rczA1[A:184-262] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Tight junction protein ZO-1 ; X-RAY DIFFRACTION 1.700Å

e2rczB1[B:184-264] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Tight junction protein ZO-1 ; X-RAY DIFFRACTION 1.700Å

e2jweA1[A:1-82] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

TIGHT JUNCTION PROTEIN ZO-1 ; SOLUTION NMR

e2jweB1[B:1-82] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

TIGHT JUNCTION PROTEIN ZO-1 ; SOLUTION NMR

e3cyyB1[B:183-263] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Tight junction protein ZO-1 ; X-RAY DIFFRACTION 2.4Å

e3fy5B1[B:253-341] Image Pymol Jmol Links: PDB, SCOP, CATH

SEGMENT POLARITY PROTEIN DISHEVELLED HOMOLOG DVL- 2 ; X-RAY DIFFRACTION 2.4Å

e2ka9A1[A:1-94] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Disks large homolog 4 ; SOLUTION NMR

e3gslB1[B:61-154] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DISKS LARGE HOMOLOG 4 ; X-RAY DIFFRACTION 2.05Å

e3i4wB1[B:305-402] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Disks large homolog 4 ; ligands: ACT ; X-RAY DIFFRACTION 1.350Å

e3i4wC1[C:305-402] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Disks large homolog 4 ; ligands: ACT ; X-RAY DIFFRACTION 1.350Å

e3i4wD1[D:305-402] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Disks large homolog 4 ; ligands: ACT ; X-RAY DIFFRACTION 1.350Å

e3k82A1[A:305-402] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Disks large homolog 4 ; ligands: EPE,GOL,PO4 ; X-RAY DIFFRACTION 1.400Å

e3jxtB1[B:399-493] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Disks large homolog 3 ; ligands: ACT ; X-RAY DIFFRACTION 1.50Å

e3lnxB1[B:1-94] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI