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:
e1jetA3[A:1-45,A:166-269,A:486-517] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
OLIGO-PEPTIDE BINDING PROTEIN ; ligands: IUM ; X-RAY DIFFRACTION 1.2Å
e1jetA4[A:270-485] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
OLIGO-PEPTIDE BINDING PROTEIN ; ligands: IUM ; X-RAY DIFFRACTION 1.2Å
e3rybA1[A:13-70,A:195-299,A:543-575] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
OLIGOPEPTIDE-BINDING PROTEIN OPPA ; X-RAY DIFFRACTION 1.5Å
e3rybA2[A:300-542] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
OLIGOPEPTIDE-BINDING PROTEIN OPPA ; X-RAY DIFFRACTION 1.5Å
e1xocA3[A:17-54,A:158-263,A:490-520] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Oligopeptide-binding protein appA ; ligands: ZN ; X-RAY DIFFRACTION 1.55Å
e4oetA2[A:1-35,A:137-238,A:461-494] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Putative peptide ABC-transport system periplasmic peptide-binding protein ; ligands: GOL ; X-RAY DIFFRACTION 2.40Å
e4oetB2[B:1-35,B:137-238,B:461-494] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Putative peptide ABC-transport system periplasmic peptide-binding protein ; ligands: GOL ; X-RAY DIFFRACTION 2.40Å
e4oeuA4[A:2-35,A:137-238,A:461-494] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Putative peptide ABC-transport system periplasmic peptide-binding protein ; ligands: HIS,MG,NI,PEG ; X-RAY DIFFRACTION 2.20Å
e4oeuB2[B:2-35,B:137-238,B:461-494] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Putative peptide ABC-transport system periplasmic peptide-binding protein ; ligands: HIS,MG,NI,PEG ; X-RAY DIFFRACTION 2.20Å
e4oevA4[A:1-35,A:137-238,A:461-494] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Putative peptide ABC-transport system periplasmic peptide-binding protein ; ligands: NI,OXL ; X-RAY DIFFRACTION 1.90Å
e4oevB2[B:1-35,B:137-238,B:461-494] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Putative peptide ABC-transport system periplasmic peptide-binding protein ; ligands: GOL,NI,OXL ; X-RAY DIFFRACTION 1.90Å
e3t66A1[A:12-43,A:144-237,A:458-487] Image Pymol Jmol Links: PDB, SCOP, CATH
NICKEL ABC TRANSPORTER (NICKEL-BINDING PROTEIN) ; ligands: CA ; X-RAY DIFFRACTION 2.8Å
e2d5wB1[B:1-42,B:158-184,B:208-296,B:554-602] Image Pymol Jmol Links: PDB, SCOP, CATH
PEPTIDE ABC TRANSPORTER, PEPTIDE-BINDING PROTEIN ; X-RAY DIFFRACTION 1.3Å
e2d5wA3[A:1-42,A:158-296,A:554-602] Image Pymol Jmol Links: PDB, SCOP, CATH
PEPTIDE ABC TRANSPORTER, PEPTIDE-BINDING PROTEIN ; X-RAY DIFFRACTION 1.3Å
e4tozA1[A:23-67,A:188-289,A:506-537] Image Pymol Jmol Links: PDB, SCOP, CATH
Periplasmic murein peptide-binding protein ; X-RAY DIFFRACTION 1.5Å
e4tozB2[B:26-67,B:188-289,B:506-540] Image Pymol Jmol Links: PDB, SCOP, CATH
Periplasmic murein peptide-binding protein ; X-RAY DIFFRACTION 1.5Å
e4ra1A2[A:32-65,A:182-282] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
ABC transporter, substrate binding protein (Agrocinopines A and B) ; ligands: ALX,BNX,EDO ; X-RAY DIFFRACTION 1.75Å
e4ze8A1[A:31-65,A:182-282] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
ABC transporter, substrate binding protein (Agrocinopines A and B) ; ligands: SO4 ; X-RAY DIFFRACTION 1.710Å
e4ze8B3[B:31-65,B:182-282] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
ABC transporter, substrate binding protein (Agrocinopines A and B) ; ligands: EDO ; X-RAY DIFFRACTION 1.710Å
e4ze8C3[C:31-65,C:182-282] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
ABC transporter, substrate binding protein (Agrocinopines A and B) ; X-RAY DIFFRACTION 1.710Å
e4ze8D3[D:31-65,D:182-282] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
ABC transporter, substrate binding protein (Agrocinopines A and B) ; ligands: EDO ; X-RAY DIFFRACTION 1.710Å
e4ze9A2[A:32-65,A:182-282] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
ABC transporter substrate-binding protein ; ligands: AGR ; X-RAY DIFFRACTION 2.650Å
e4zebA2[A:32-65,A:182-282] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
ABC transporter, substrate binding protein (Agrocinopines A and B) ; ligands: AGR,EDO ; X-RAY DIFFRACTION 1.890Å
e4zebB3[B:32-65,B:182-282] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
ABC transporter, substrate binding protein (Agrocinopines A and B) ; ligands: AGR,PEG ; X-RAY DIFFRACTION 1.890Å
e4zecA2[A:32-65,A:182-282] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
ABC transporter, substrate binding protein (Agrocinopines A and B) ; ligands: C84,EDO ; X-RAY DIFFRACTION 2.147Å
e4zedA3[A:32-65,A:182-282] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
ABC transporter, substrate binding protein (Agrocinopines A and B) ; ligands: AGW ; X-RAY DIFFRACTION 1.750Å
e4zeiA1[A:32-65,A:182-282] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
ABC transporter, substrate binding protein (Agrocinopines A and B) ; ligands: EDO,LAO ; X-RAY DIFFRACTION 2.300Å
e4zekA2[A:32-65,A:182-282] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
ABC TRANSPORTER, SUBSTRATE BINDING PROTEIN (AGROCINOPINES A AND B) ; ligands: EDO,LAH ; X-RAY DIFFRACTION 2.10Å
e5f1qA1[A:29-43,A:185-289,A:507-541] Image Pymol Jmol Links: PDB, SCOP, CATH
Periplasmic dipeptide transport protein ; ligands: EDO,GLN ; X-RAY DIFFRACTION 1.95Å
e5f1qB2[B:29-43,B:185-289,B:507-535] Image Pymol Jmol Links: PDB, SCOP, CATH
Periplasmic dipeptide transport protein ; ligands: EDO,GLN ; X-RAY DIFFRACTION 1.95Å
e5isuA3[A:37-72,A:175-277,A:491-524] Image Pymol Jmol Links: PDB, SCOP, CATH
Lmo0135 protein ; ligands: EDO ; X-RAY DIFFRACTION 2.20Å
e5kztA2[A:42-77,A:198-299,A:528-559] Image Pymol Jmol Links: PDB, SCOP, CATH
Peptide/nickel transport system substrate-binding protein ; X-RAY DIFFRACTION 1.85Å
e5kztB2[B:41-77,B:198-299,B:528-559] Image Pymol Jmol Links: PDB, SCOP, CATH
Peptide/nickel transport system substrate-binding protein ; X-RAY DIFFRACTION 1.85Å
e5icqA2[A:35-97,A:202-315,A:575-609] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Methylocystis parvus OBBP MbnE ; ligands: SO4 ; X-RAY DIFFRACTION 1.9Å
e5hm4B1[B:21-59,B:162-271,B:518-560] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Mannoside ABC transport system, sugar-binding protein ; X-RAY DIFFRACTION 2.0Å
e5mwuA3[A:2-19,A:141-245,A:471-499] Image Pymol Jmol Links: PDB, SCOP, CATH
Nickel-binding periplasmic protein ; ligands: ACT,EDT,GOL ; X-RAY DIFFRACTION 1.8Å
e5mwuB3[B:3-19,B:141-245,B:471-500] Image Pymol Jmol Links: PDB, SCOP, CATH
Nickel-binding periplasmic protein ; ligands: 6RP,ACT,CL,GOL ; X-RAY DIFFRACTION 1.8Å
e5u4oA1[A:42-77,A:181-279,A:493-521] Image Pymol Jmol Links: PDB, SCOP, CATH
ABC transporter substrate-binding protein ; X-RAY DIFFRACTION 2.05Å
e5l8dA1[A:2-19,A:141-245,A:471-499] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Nickel-binding periplasmic protein ; ligands: ACT,EDT,GOL ; X-RAY DIFFRACTION 1.8Å
e5l8dB1[B:3-19,B:141-245,B:471-500] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Nickel-binding periplasmic protein ; ligands: 6RP,ACT,CL,GOL ; X-RAY DIFFRACTION 1.8Å
e2wolA3[A:8-71,A:200-307,A:536-560] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
CLAVULANIC ACID BIOSYNTHESIS OLIGOPEPTIDE BINDING PROTEIN 2 ; ligands: GOL ; X-RAY DIFFRACTION 1.45Å
e1xocA4[A:264-489] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Oligopeptide-binding protein appA ; ligands: ZN ; X-RAY DIFFRACTION 1.55Å
e3o6pA1[A:300-526] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH
Peptide ABC transporter, peptide-binding protein ; ligands: NA ; X-RAY DIFFRACTION 1.65Å
e1vr5A3[A:23-59,A:162-271,A:516-557] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH
oligopeptide ABC transporter, periplasmic oligopeptide-binding protein ; ligands: ACT,EDO ; X-RAY DIFFRACTION 1.730Å
e1vr5A4[A:272-515] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH
oligopeptide ABC transporter, periplasmic oligopeptide-binding protein ; ligands: EDO,EPE,FMT,NA ; X-RAY DIFFRACTION 1.730Å
e1zlqA3[A:246-470] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
NICKEL-BINDING PERIPLASMIC PROTEIN ; ligands: ACT,CL,EDT,GOL,SO4 ; X-RAY DIFFRACTION 1.8Å
e1zlqA4[A:3-19,A:141-245,A:471-501] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
NICKEL-BINDING PERIPLASMIC PROTEIN ; ligands: ACT,CL,EDT,GOL ; X-RAY DIFFRACTION 1.8Å
e3lvuA1[A:311-568] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH
ABC transporter, periplasmic substrate-binding protein ; ligands: GOL,IOD ; X-RAY DIFFRACTION 1.80Å
e4onyA1[A:12-85,A:191-304,A:565-594] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH
Extracellular solute-binding protein family 5 ; ligands: GOL,P4G ; X-RAY DIFFRACTION 2.100Å
e4onyA3[A:305-564] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH
Extracellular solute-binding protein family 5 ; ligands: CL ; X-RAY DIFFRACTION 2.100Å
e3pamA1[A:319-574] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH
Transmembrane protein ; ligands: EOH ; X-RAY DIFFRACTION 2.31Å
e2grvC2[C:277-566] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
LpqW ; X-RAY DIFFRACTION 2.4Å
e5ipwA2[A:360-621] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Oligopeptide ABC transporter, periplasmic oligopeptide-binding protein, putative ; X-RAY DIFFRACTION 2.6Å
e1uqwA3[A:242-460] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH
PUTATIVE BINDING PROTEIN YLIB ; ligands: GOL,ZN ; X-RAY DIFFRACTION 2.72Å
e1uqwA4[A:3-37,A:142-241,A:461-489] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH
PUTATIVE BINDING PROTEIN YLIB ; ligands: GOL,ZN ; X-RAY DIFFRACTION 2.72Å
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