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
beta meanderssingle beta-sheet with mainly meander topology
beta sandwichestwo beta-sheets stacked together to form a sandwich
beta duplicates or obligate multimersbeta duplicates or monomers associate together to form a compact domain
beta complex topologybeta domains with complex and unique topology that cannot be described as barrel or sandwich or meander
a+b two layersone alpha-helix layer and one beta-sheet layer
a+b three layersone mainly antiparallel beta-sheet layer sandwiched between two alpha-helix layers
a+b four layerstwo beta-sheet layers sandwiched between two alpha-helix layers
a+b complex topologyalpha and beta domain with complex and unique topology that cannot be described in layers
a+b duplicates or obligate multimersalpha and beta duplicates or monomers associated together to form a compact domain
a/b barrelsrepeating beta-alpha units form a barrel
a/b three-layered sandwichesrepeating beta-alpha units form a sandwich with a mainly parallel beta-sheet layer stacked between two alpha-helix layers
Representatives:
e1ii5A2[A:1-94,A:188-226] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Slr1257 protein ; ligands: GLU ; X-RAY DIFFRACTION 1.6Å
e4z9nB1[B:2-102,B:205-321] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH
Amino acid ABC transporter, periplasmic amino acid-binding protein ; ligands: EDO,GSH,NA ; X-RAY DIFFRACTION 1.745Å
e4p0iB1[B:27-114,B:238-282] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Nopaline-binding periplasmic protein ; ligands: EDO ; X-RAY DIFFRACTION 1.89Å
e5sv6A1[A:36-116,A:240-281] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Extracellular solute-binding protein, family 3 ; X-RAY DIFFRACTION 1.92Å
e1xt8A2[A:10-108,A:203-257] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
putative amino-acid transporter periplasmic solute-binding protein ; ligands: CYS ; X-RAY DIFFRACTION 2.00Å
e5gzsA1[A:48-122,A:209-255] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
GGDEF family protein ; ligands: ARG ; X-RAY DIFFRACTION 2.601Å
e5gzsA3[A:256-355,A:457-491] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
GGDEF family protein ; X-RAY DIFFRACTION 2.601Å
e1lstA2[A:1-90,A:191-238] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed,
LYSINE, ARGININE, ORNITHINE-BINDING PROTEIN ; ligands: LYS ; X-RAY DIFFRACTION
e1wdnA2[A:4-87,A:184-226] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
GLUTAMINE BINDING PROTEIN ; ligands: GLN ; X-RAY DIFFRACTION
e4c0rA1[A:1-87,A:190-239] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
PUTATIVE AMINO ACID BINDING PROTEIN ; ligands: CD,CL,GDS ; X-RAY DIFFRACTION 1.55Å
e4c0rB2[B:3-87,B:190-240] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
PUTATIVE AMINO ACID BINDING PROTEIN ; ligands: CD,CL,GDS ; X-RAY DIFFRACTION 1.55Å
e4eq9A2[A:37-123,A:224-276] Image Pymol Jmol Links: PDB, SCOP, CATH
ABC transporter substrate-binding protein-amino acid transport ; ligands: GSH ; X-RAY DIFFRACTION 1.40Å
e4f3pA2[A:26-110,A:207-247] Image Pymol Jmol Links: PDB, SCOP, CATH
Glutamine-binding periplasmic protein ; X-RAY DIFFRACTION 2.400Å
e4f3pB1[B:26-110,B:207-296] Image Pymol Jmol Links: PDB, SCOP, CATH
Glutamine-binding periplasmic protein ; X-RAY DIFFRACTION 2.400Å
e4f3sA1[A:4-94,A:197-234] Image Pymol Jmol Links: PDB, SCOP, CATH
Putative periplasmic binding protein ; ligands: DAL,GLY,PO4 ; X-RAY DIFFRACTION 2.14Å
e4g4pA2[A:10-108,A:205-244] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Amino acid ABC transporter, amino acid-binding/permease protein ; ligands: GLN ; X-RAY DIFFRACTION 1.35Å
e1gggA2[A:5-87,A:184-224] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
GLUTAMINE BINDING PROTEIN ; X-RAY DIFFRACTION 2.3Å
e1gggB1[B:5-87,B:184-224] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
GLUTAMINE BINDING PROTEIN ; X-RAY DIFFRACTION 2.3Å
e4gvoA2[A:34-121,A:223-269] Image Pymol Jmol Links: PDB, SCOP, CATH
LMO2349 PROTEIN ; ligands: CL,CSX,HIS,NA ; X-RAY DIFFRACTION 1.45Å
e4gvoB2[B:34-121,B:223-269] Image Pymol Jmol Links: PDB, SCOP, CATH
LMO2349 PROTEIN ; ligands: CL,CSX,HIS,NA ; X-RAY DIFFRACTION 1.45Å
e4h5fA2[A:30-128,A:227-269] Image Pymol Jmol Links: PDB, SCOP, CATH
AMINO ACID ABC SUPERFAMILY ATP BINDING CASSETTE TRANSPORTER, BINDING PROTEIN ; ligands: ARG,GOL,PEG,PGE,SO4 ; X-RAY DIFFRACTION 1.9Å
e4h5fB1[B:30-128,B:227-269] Image Pymol Jmol Links: PDB, SCOP, CATH
AMINO ACID ABC SUPERFAMILY ATP BINDING CASSETTE TRANSPORTER, BINDING PROTEIN ; ligands: ACT,ARG,EDO,PEG,PGE,SO4 ; X-RAY DIFFRACTION 1.9Å
e4h5fC1[C:30-128,C:227-269] Image Pymol Jmol Links: PDB, SCOP, CATH
AMINO ACID ABC SUPERFAMILY ATP BINDING CASSETTE TRANSPORTER, BINDING PROTEIN ; ligands: ACT,ARG,GOL,PEG,PGE,SO4 ; X-RAY DIFFRACTION 1.9Å
e4h5fD2[D:31-128,D:227-269] Image Pymol Jmol Links: PDB, SCOP, CATH
AMINO ACID ABC SUPERFAMILY ATP BINDING CASSETTE TRANSPORTER, BINDING PROTEIN ; ligands: ARG,GOL,PEG ; X-RAY DIFFRACTION 1.9Å
e4h5gA2[A:30-128,A:227-269] Image Pymol Jmol Links: PDB, SCOP, CATH
Amino acid ABC superfamily ATP binding cassette transporter, binding protein ; ligands: ACT,ARG,EDO,GOL,PEG ; X-RAY DIFFRACTION 1.78Å
e4h5gB1[B:30-128,B:227-269] Image Pymol Jmol Links: PDB, SCOP, CATH
Amino acid ABC superfamily ATP binding cassette transporter, binding protein ; ligands: ARG,EDO,GOL,PEG,SO4 ; X-RAY DIFFRACTION 1.78Å
e3h7mA1[A:52-140,A:237-279] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Sensor protein ; ligands: NA ; X-RAY DIFFRACTION 2.400Å
e3i6vA1[A:52-136,A:225-269] Image Pymol Jmol Links: PDB, SCOP, CATH
periplasmic His/Glu/Gln/Arg/opine family-binding protein ; ligands: GOL,LYS,NA ; X-RAY DIFFRACTION 2.000Å
e4i62A2[A:31-126,A:226-268] Image Pymol Jmol Links: PDB, SCOP, CATH
AMINO ACID ABC TRANSPORTER, PERIPLASMIC AMINO ACID-BINDING PROTEIN, PUTATIVE ; ligands: ARG,CL ; X-RAY DIFFRACTION 1.05Å
e2ieeB1[B:14-110,B:208-262] Image Pymol Jmol Links: PDB, SCOP, CATH
Probable ABC transporter extracellular-binding protein yckB ; X-RAY DIFFRACTION 2.2Å
e3k4uA1[A:1-88,A:188-233] Image Pymol Jmol Links: PDB, SCOP, CATH
BINDING COMPONENT OF ABC TRANSPORTER ; ligands: LYS ; X-RAY DIFFRACTION 2.620Å
e3k4uB1[B:1-88,B:188-233] Image Pymol Jmol Links: PDB, SCOP, CATH
BINDING COMPONENT OF ABC TRANSPORTER ; ligands: LYS ; X-RAY DIFFRACTION 2.620Å
e3k4uC2[C:1-88,C:188-233] Image Pymol Jmol Links: PDB, SCOP, CATH
BINDING COMPONENT OF ABC TRANSPORTER ; ligands: LYS ; X-RAY DIFFRACTION 2.620Å
e3k4uD1[D:1-88,D:188-233] Image Pymol Jmol Links: PDB, SCOP, CATH
BINDING COMPONENT OF ABC TRANSPORTER ; ligands: LYS ; X-RAY DIFFRACTION 2.620Å
e3k4uE2[E:0-88,E:188-233] Image Pymol Jmol Links: PDB, SCOP, CATH
BINDING COMPONENT OF ABC TRANSPORTER ; ligands: LYS ; X-RAY DIFFRACTION 2.620Å
e3k4uF2[F:1-88,F:188-233] Image Pymol Jmol Links: PDB, SCOP, CATH
BINDING COMPONENT OF ABC TRANSPORTER ; ligands: LYS ; X-RAY DIFFRACTION 2.620Å
e4kqpA1[A:255-345,A:442-484] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Glutamine ABC transporter permease and substrate binding protein protein ; ligands: GLN ; X-RAY DIFFRACTION 0.95Å
e4kr5A2[A:253-345,A:442-481] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Glutamine ABC transporter permease and substrate binding protein protein ; ligands: CL,MG,PEG ; X-RAY DIFFRACTION 1.5Å
e4kr5B2[B:253-345,B:442-484] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Glutamine ABC transporter permease and substrate binding protein protein ; ligands: CL,MG ; X-RAY DIFFRACTION 1.5Å
e3mpkA1[A:292-392,A:490-526] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Virulence sensor protein bvgS ; ligands: ACT,GOL ; X-RAY DIFFRACTION 2.04Å
e3mplA2[A:292-392,A:490-526] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
VIRULENCE SENSOR PROTEIN BVGS ; ligands: EDO ; X-RAY DIFFRACTION 2.1Å
e2o1mA2[A:14-103,A:204-245] Image Pymol Jmol Links: PDB, SCOP, CATH
Probable amino-acid ABC transporter extracellular-binding protein ytmK ; ligands: SO4 ; X-RAY DIFFRACTION 2.0Å
e2o1mB2[B:14-103,B:204-243] Image Pymol Jmol Links: PDB, SCOP, CATH
Probable amino-acid ABC transporter extracellular-binding protein ytmK ; ligands: SO4 ; X-RAY DIFFRACTION 2.0Å
e4oenA2[A:268-352,A:448-487] Image Pymol Jmol Links: PDB, SCOP, CATH
SECOND SUBSTRATE BINDING DOMAIN OF PUTATIVE AMINO ACID ABC TRANSPORTER ; ligands: ACT,CL,SO4 ; X-RAY DIFFRACTION 1.65Å
e4oenB2[B:266-352,B:448-487] Image Pymol Jmol Links: PDB, SCOP, CATH
SECOND SUBSTRATE BINDING DOMAIN OF PUTATIVE AMINO ACID ABC TRANSPORTER ; ligands: ACT,CL ; X-RAY DIFFRACTION 1.65Å
e2pvuA1[A:17-105,A:204-251] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
ArtJ ; ligands: LYS,SO4 ; X-RAY DIFFRACTION 1.79Å
e2pyyA2[A:4-87,A:183-221] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
IONOTROPIC GLUTAMATE RECEPTOR BACTERIAL HOMOLOGUE ; ligands: GLU ; X-RAY DIFFRACTION 2.1Å
e2pyyB1[B:4-87,B:183-226] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
IONOTROPIC GLUTAMATE RECEPTOR BACTERIAL HOMOLOGUE ; ligands: GLU ; X-RAY DIFFRACTION 2.1Å
e2pyyC2[C:4-87,C:183-221] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
IONOTROPIC GLUTAMATE RECEPTOR BACTERIAL HOMOLOGUE ; ligands: GLU ; X-RAY DIFFRACTION 2.1Å
e2q2aA1[A:11-105,A:204-251] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
ArtJ ; ligands: ARG,SO4 ; X-RAY DIFFRACTION 1.620Å
e2q2aB1[B:11-105,B:204-251] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
ArtJ ; ligands: ARG,SO4 ; X-RAY DIFFRACTION 1.620Å
e2q2aC1[C:11-105,C:204-251] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
ArtJ ; ligands: ARG,SO4 ; X-RAY DIFFRACTION 1.620Å
e2q2aD1[D:11-105,D:204-251] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
ArtJ ; ligands: ARG,SO4 ; X-RAY DIFFRACTION 1.620Å
e2q2cA1[A:21-105,A:204-251] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
ArtJ ; ligands: HIS,SO4 ; X-RAY DIFFRACTION 2.350Å
e2q2cB1[B:21-105,B:204-251] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
ArtJ ; ligands: HIS,SO4 ; X-RAY DIFFRACTION 2.350Å
e2q2cC1[C:21-105,C:204-251] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
ArtJ ; ligands: GOL,HIS,SO4 ; X-RAY DIFFRACTION 2.350Å
e2q2cD1[D:21-105,D:204-251] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
ArtJ ; ligands: HIS,SO4 ; X-RAY DIFFRACTION 2.350Å
e2v25A2[A:3-101,A:197-233] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
MAJOR CELL-BINDING FACTOR ; ligands: ASP,ZN ; X-RAY DIFFRACTION 1.49Å
e4prsA1[A:1-94,A:189-226] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
ABC-type transporter, periplasmic subunit family 3 ; X-RAY DIFFRACTION 1.47Å
e4prsB2[B:1-94,B:189-227] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
ABC-type transporter, periplasmic subunit family 3 ; X-RAY DIFFRACTION 1.47Å
e4pshA1[A:2-94,A:189-226] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
ABC-type transporter, periplasmic subunit family 3 ; ligands: ARG ; X-RAY DIFFRACTION 2.6Å
e4pshB2[B:1-94,B:189-226] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
ABC-type transporter, periplasmic subunit family 3 ; ligands: ARG ; X-RAY DIFFRACTION 2.6Å
e8eyzA1[A:1-87,A:184-226] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Amino acid ABC transporter substrate-binding protein ; ligands: GLN,SO4,X5Z ; X-RAY DIFFRACTION 2.99Å
e8eyzB2[B:3-87,B:184-223] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Amino acid ABC transporter substrate-binding protein ; ligands: GLN,SO4,X5Z ; X-RAY DIFFRACTION 2.99Å
e8eyzC2[C:4-87,C:184-222] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Amino acid ABC transporter substrate-binding protein ; ligands: GLN,SO4,X5Z ; X-RAY DIFFRACTION 2.99Å
e8eyzD2[D:3-87,D:184-223] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Amino acid ABC transporter substrate-binding protein ; ligands: GLN,GOL,X5Z ; X-RAY DIFFRACTION 2.99Å
e8eyzE2[E:2-87,E:184-225] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Amino acid ABC transporter substrate-binding protein ; ligands: GLN,X5Z ; X-RAY DIFFRACTION 2.99Å
e8eyzF2[F:3-87,F:184-225] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Amino acid ABC transporter substrate-binding protein ; ligands: GLN,GOL,X5Z ; X-RAY DIFFRACTION 2.99Å
e8eyzG1[G:3-87,G:184-224] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Amino acid ABC transporter substrate-binding protein ; ligands: GLN,SO4,X5Z ; X-RAY DIFFRACTION 2.99Å
e8eyzH2[H:4-87,H:184-224] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Amino acid ABC transporter substrate-binding protein ; ligands: GLN,X5Z ; X-RAY DIFFRACTION 2.99Å
e8eyzI2[I:4-87,I:184-226] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Amino acid ABC transporter substrate-binding protein ; ligands: GLN,X5Z ; X-RAY DIFFRACTION 2.99Å
e8eyzJ1[J:3-87,J:184-224] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Amino acid ABC transporter substrate-binding protein ; ligands: GLN,X5Z ; X-RAY DIFFRACTION 2.99Å
e8eyzK1[K:3-87,K:184-226] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Amino acid ABC transporter substrate-binding protein ; ligands: GLN,X5Z ; X-RAY DIFFRACTION 2.99Å
e8eyzL1[L:4-87,L:184-223] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Amino acid ABC transporter substrate-binding protein ; ligands: GLN,X5Z ; X-RAY DIFFRACTION 2.99Å
Pseudo group of domains that do not map to PFam family profiles. Domains inside should not be considered as in one family.
mixed a+b and a/balpha and beta domain consists of both a+b and a/b regions
few secondary structure elementsstabilized by cofactors or disulfides
extended segmentsextended, non-globular segments, frequently bind to other proteins to form complexes