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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

X: alpha-helical domain in beta-lactamase/transpeptidase-like proteins
H: alpha-helical domain in beta-lactamase/transpeptidase-like proteins
T: alpha-helical domain in beta-lactamase/transpeptidase-like proteins
F: Transpeptidase

PF00905 CL0013

Representatives:

e1k55A1[A:63-160] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

BETA LACTAMASE OXA-10 ; ligands: EDO,SO4 ; X-RAY DIFFRACTION 1.39Å

e1k38A1[A:63-160] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

BETA-LACTAMASE OXA-2 ; ligands: FMT ; X-RAY DIFFRACTION 1.5Å

e1m6kA1[A:63-166] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

BETA-LACTAMASE OXA-1 ; ligands: MPD ; X-RAY DIFFRACTION 1.5Å

e3udfA3[A:431-530] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Penicillin-binding protein 1a ; ligands: MES ; X-RAY DIFFRACTION 1.7Å

e1vqqA1[A:400-525] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed,

PENICILLIN-BINDING PROTEIN MECA, LOW-AFFINITY ; X-RAY DIFFRACTION 1.8Å

e1xa1A1[A:56-151] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

REGULATORY PROTEIN BLAR1 ; ligands: PO4,POP ; X-RAY DIFFRACTION 1.8Å

e5crfA2[A:342-455] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Penicillin-binding protein 1A ; ligands: PO4 ; X-RAY DIFFRACTION 1.8Å

e2bg1A1[A:457-561] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PENICILLIN-BINDING PROTEIN 1B ; X-RAY DIFFRACTION 1.900Å

e4r1gA3[A:679-808] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

Peptidoglycan glycosyltransferase ; ligands: CXU ; X-RAY DIFFRACTION 1.92Å

e3zg8B3[B:391-493] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PENICILLIN-BINDING PROTEIN 4 ; ligands: AIX,GOL ; X-RAY DIFFRACTION 2.09Å

e2waeA4[A:383-522] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PENICILLIN-BINDING PROTEIN 2B ; X-RAY DIFFRACTION 2.26Å

e3oclA3[A:291-411] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PENICILLIN-BINDING PROTEIN 3 ; ligands: CB9,CL ; X-RAY DIFFRACTION 2.3Å

e1pyyA2[A:334-455] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Penicillin-binding protein 2X ; ligands: OSU,SO4 ; X-RAY DIFFRACTION 2.42Å

e1nrfA1[A:399-494] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

REGULATORY PROTEIN BLAR1 ; X-RAY DIFFRACTION 2.44Å

e2c5wB1[B:367-470] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PENICILLIN-BINDING PROTEIN 1A ; ligands: CL,EDO,PCZ,ZN ; X-RAY DIFFRACTION 2.550Å

e3pbnA1[A:288-411] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Penicillin-binding protein 3 ; X-RAY DIFFRACTION 2Å

e2fffB1[B:456-560] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PENICILLIN-BINDING PROTEIN 1B ; X-RAY DIFFRACTION 2.23Å

e2uwxA1[A:456-560] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PENICILLIN-BINDING PROTEIN 1B ; X-RAY DIFFRACTION 2.39Å

e2xd1B1[B:457-561] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PENICILLIN-BINDING PROTEIN 1B ; ligands: CEF ; X-RAY DIFFRACTION 3.00Å

e2c6wB1[B:366-469] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PENICILLIN-BINDING PROTEIN 1A ; ligands: CL,ZN ; X-RAY DIFFRACTION 2.61Å

e3udiA2[A:431-530] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PENICILLIN-BINDING PROTEIN 1A ; ligands: PNM ; X-RAY DIFFRACTION 2.6Å

e3udiB2[B:431-530] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PENICILLIN-BINDING PROTEIN 1A ; ligands: PNM ; X-RAY DIFFRACTION 2.6Å

e3udxA2[A:431-530] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PENICILLIN-BINDING PROTEIN 1A ; ligands: IM2 ; X-RAY DIFFRACTION 2.5Å

e3udxB2[B:431-530] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PENICILLIN-BINDING PROTEIN 1A ; ligands: IM2 ; X-RAY DIFFRACTION 2.5Å

e3ue0A2[A:431-530] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PENICILLIN-BINDING PROTEIN 1A ; ligands: AZR ; X-RAY DIFFRACTION 2.6Å

e3ue0B2[B:431-530] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PENICILLIN-BINDING PROTEIN 1A ; ligands: AZR ; X-RAY DIFFRACTION 2.6Å

e3ue1A2[A:431-530] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Penicillin-binding protein 1a ; ligands: UE1 ; X-RAY DIFFRACTION 2.7Å

e3ue1B2[B:431-530] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Penicillin-binding protein 1a ; ligands: UE1 ; X-RAY DIFFRACTION 2.7Å

e3upoB3[B:219-343] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PENICILLIN-BINDING PROTEIN A ; ligands: PNM ; X-RAY DIFFRACTION 2.3Å

e3un7B3[B:219-343] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PENICILLIN-BINDING PROTEIN A ; X-RAY DIFFRACTION 2.0Å

e3un7A3[A:219-343] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PENICILLIN-BINDING PROTEIN A ; X-RAY DIFFRACTION 2.0Å

e3uppB3[B:219-343] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Penicillin-binding protein A ; ligands: PCZ ; X-RAY DIFFRACTION 2.4Å

e3lo7A3[A:218-343] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Penicillin-binding protein A ; X-RAY DIFFRACTION 2.05Å

e2zc5D3[D:367-470] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Penicillin-binding protein 1A ; ligands: BMG,ZN ; X-RAY DIFFRACTION 3.00Å

e2zc6B3[B:367-470] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Penicillin-binding protein 1A ; ligands: TEB,ZN ; X-RAY DIFFRACTION 2.70Å

e2zc6D3[D:367-470] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Penicillin-binding protein 1A ; ligands: TEB,ZN ; X-RAY DIFFRACTION 2.70Å

e2zc5B3[B:367-470] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Penicillin-binding protein 1A ; ligands: BMG,ZN ; X-RAY DIFFRACTION 3.00Å

e2xd5A3[A:457-561] Image Pymol Jmol Links: PDB, SCOP, CATH

PENICILLIN-BINDING PROTEIN 1B ; ligands: S2D ; X-RAY DIFFRACTION 2.5Å

e2y2oA3[A:457-561] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PENICILLIN-BINDING PROTEIN 1B ; ligands: CL,EO9 ; X-RAY DIFFRACTION 1.88Å

e2y2qB3[B:457-561] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PENICILLIN-BINDING PROTEIN 1B ; ligands: CL,Z06 ; X-RAY DIFFRACTION 2.15Å

e2xd1A3[A:457-561] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PENICILLIN-BINDING PROTEIN 1B ; ligands: CEF ; X-RAY DIFFRACTION 3.00Å

e2jchA3[A:457-561] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PENICILLIN-BINDING PROTEIN 1B ; ligands: PL7 ; X-RAY DIFFRACTION 2.4Å

e2je5B1[B:457-561] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PENICILLIN-BINDING PROTEIN 1B ; ligands: L4C ; X-RAY DIFFRACTION 2.6Å

e2xd5B3[B:457-561] Image Pymol Jmol Links: PDB, SCOP, CATH

PENICILLIN-BINDING PROTEIN 1B ; ligands: S2D ; X-RAY DIFFRACTION 2.5Å

e2y2hA3[A:457-561] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PENICILLIN-BINDING PROTEIN 1B ; ligands: CL,NA,ZA2 ; X-RAY DIFFRACTION 1.96Å

e2y2hB3[B:457-561] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PENICILLIN-BINDING PROTEIN 1B ; ligands: CL,ZA2 ; X-RAY DIFFRACTION 1.96Å

e2y2iA3[A:457-561] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PENICILLIN-BINDING PROTEIN 1B ; ligands: CL,NA,ZA3 ; X-RAY DIFFRACTION 1.78Å

e2y2jA3[A:457-561] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PENICILLIN-BINDING PROTEIN 1B ; ligands: CL,EDO,ZA4 ; X-RAY DIFFRACTION 2.06Å

e2y2kA3[A:457-561] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PENICILLIN-BINDING PROTEIN 1B ; ligands: CL,EDO,ZA5 ; X-RAY DIFFRACTION 2.09Å

e2y2lA3[A:457-561] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PENICILLIN-BINDING PROTEIN 1B ; ligands: CL,E06 ; X-RAY DIFFRACTION 2.07Å

e2y2lB3[B:457-561] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PENICILLIN-BINDING PROTEIN 1B ; ligands: CL,E06 ; X-RAY DIFFRACTION 2.07Å

e2y2mA3[A:457-561] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PENICILLIN-BINDING PROTEIN 1B ; ligands: CL,E08 ; X-RAY DIFFRACTION 1.62Å

e2y2nA3[A:457-561] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PENICILLIN-BINDING PROTEIN 1B ; ligands: CL,E07 ; X-RAY DIFFRACTION 2.07Å

e2y2qA3[A:457-561] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PENICILLIN-BINDING PROTEIN 1B ; ligands: CL,EDO,NA,Z06 ; X-RAY DIFFRACTION 2.15Å

e2y2gA3[A:457-561] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PENICILLIN-BINDING PROTEIN 1B ; ligands: A01,CL,EDO ; X-RAY DIFFRACTION 2.05Å

e2y2gB3[B:457-561] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PENICILLIN-BINDING PROTEIN 1B ; ligands: A01,CL ; X-RAY DIFFRACTION 2.05Å

e2y2pA3[A:457-561] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PENICILLIN-BINDING PROTEIN 1B ; ligands: CL,Z10 ; X-RAY DIFFRACTION 1.62Å

e2je5A1[A:457-561] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PENICILLIN-BINDING PROTEIN 1B ; ligands: L4C ; X-RAY DIFFRACTION 2.6Å

e3upoA3[A:219-343] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PENICILLIN-BINDING PROTEIN A ; ligands: PNM ; X-RAY DIFFRACTION 2.3Å

e3upnA3[A:219-343] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PENICILLIN-BINDING PROTEIN A ; ligands: IM2 ; X-RAY DIFFRACTION 2.2Å

e3lo7B2[B:218-341] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Penicillin-binding protein A ; X-RAY DIFFRACTION 2.05Å

e3uppA2[A:219-343] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Penicillin-binding protein A ; ligands: PCZ ; X-RAY DIFFRACTION 2.4Å

e4r3jB1[B:679-807] Image Pymol Jmol Links: PDB, SCOP, CATH

Peptidoglycan glycosyltransferase ; ligands: CFU ; X-RAY DIFFRACTION 2.44Å

e4ovdA1[A:302-421] Image Pymol Jmol Links: PDB, SCOP, CATH

Peptidoglycan glycosyltransferase ; ligands: CA ; X-RAY DIFFRACTION 2.00Å

e4mnrA2[A:179-315] Image Pymol Jmol Links: PDB, SCOP, CATH

PEPTIDOGLYCAN GLYCOSYLTRANSFERASE ; ligands: ACY,MG ; X-RAY DIFFRACTION 1.65Å

e3upnB2[B:219-342] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PENICILLIN-BINDING PROTEIN A ; ligands: IM2 ; X-RAY DIFFRACTION 2.2Å

e5uy7A1[A:296-403] Image Pymol Jmol Links: PDB, SCOP, CATH

Peptidoglycan glycosyltransferase ; ligands: SO4 ; X-RAY DIFFRACTION 1.650Å

e5lp4A2[A:307-435] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Penicillin-binding protein 2 (Pbp2) ; X-RAY DIFFRACTION 3.03Å

e5lp4B1[B:307-435] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Penicillin-binding protein 2 (Pbp2) ; X-RAY DIFFRACTION 3.03Å

e5lp5B1[B:307-435] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Penicillin-binding protein 2 (Pbp2) ; X-RAY DIFFRACTION 2.74Å

e5lp5A3[A:308-437] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Penicillin-binding protein 2 (Pbp2) ; X-RAY DIFFRACTION 2.74Å

e5u2gA4[A:450-551] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

Penicillin-binding protein 1A ; ligands: SO4 ; X-RAY DIFFRACTION 2.60Å

e2oluA1[A:395-502] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PENICILLIN-BINDING PROTEIN 2 ; X-RAY DIFFRACTION 2.9Å

e4oonA1[A:458-563] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Penicillin-binding protein 1A ; ligands: 2U4 ; X-RAY DIFFRACTION 3.2Å

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.

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

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