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X - Possible homology level

H - Homology level

T - Topology level

F - Family level

* - Provisional representative


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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

X: Periplasmic binding protein-like II
H: Periplasmic binding protein-like II
T: Periplasmic binding protein-like II
F: SBP_bac_5

PF00496 CL0177

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

e1dpeA3[A:1-15,A:157-261,A:479-507] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DIPEPTIDE-BINDING PROTEIN ; X-RAY DIFFRACTION

e1dpeA4[A:262-478] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DIPEPTIDE-BINDING PROTEIN ; ligands: CD ; X-RAY DIFFRACTION

F: Unmapped domains

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