Evolutionary classification of protein domain structures
alpha arraysalpha-helix arrays with mainly perpendicular helices
Pseudo group of domains that do not map to PFam family profiles. Domains inside should not be considered as in one family.
Representatives:
e6l0oA1[A:773-843] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
DNA helicase MCM8 ; ligands: SO4 ; X-RAY DIFFRACTION 1.21Å
e6efnA2[A:12-102] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH
Sporulation killing factor maturation protein SkfB ; X-RAY DIFFRACTION 1.291Å
e3go5A4[A:221-284] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Multidomain protein with S1 RNA-binding domains ; ligands: EDO ; X-RAY DIFFRACTION 1.40Å
e1b6aA1[A:375-448] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
METHIONINE AMINOPEPTIDASE ; ligands: TN4 ; X-RAY DIFFRACTION 1.600Å
e2vxzA1[A:5-69] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
PYRSV_GP04 ; ligands: CL,GOL ; X-RAY DIFFRACTION 1.70Å
e2obpA1[A:12-92] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH
Putative DNA-binding protein ; ligands: NO3 ; X-RAY DIFFRACTION 1.700Å
e1xgsA1[A:195-271] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
METHIONINE AMINOPEPTIDASE ; X-RAY DIFFRACTION 1.75Å
e6ghoB3[B:236-294] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
UPF0413 protein GK0824 ; ligands: CL ; X-RAY DIFFRACTION 1.79Å
e2ewfA1[A:1-128] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Nicking endonuclease N.BspD6I ; ligands: BR ; X-RAY DIFFRACTION 1.84Å
e3gbgA3[A:165-218] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
TCP pilus virulence regulatory protein ; X-RAY DIFFRACTION 1.90Å
e5xfoA4[A:248-340] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
PHD finger protein 1 ; X-RAY DIFFRACTION 1.90Å
e6j28A1[A:10-96] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
N(4)-bis(aminopropyl)spermidine synthase ; X-RAY DIFFRACTION 1.90Å
e1zelA1[A:1-82] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
hypothetical protein Rv2827c ; ligands: FMT ; X-RAY DIFFRACTION 1.93Å
e5xnhA2[A:-1-90] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
N(4)-bis(aminopropyl)spermidine synthase ; X-RAY DIFFRACTION 1.95Å
e6kjgB1[B:548-671] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Dual-functional monooxygenase/methyltransferase psoF ; X-RAY DIFFRACTION 1.99Å
e1z05A1[A:10-80] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH
transcriptional regulator, ROK family ; ligands: SO4 ; X-RAY DIFFRACTION 2.0Å
e6ahtB1[B:4-116] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Conserved hypothetical plasmid protein ; X-RAY DIFFRACTION 2.0Å
e3m8eA1[A:-15-102] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Putative DNA-binding protein ; X-RAY DIFFRACTION 2.000Å
e7bdvA3[A:157-237] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Can2 ; X-RAY DIFFRACTION 2.02Å
e2qm3A1[A:1-87] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH
PREDICTED METHYLTRANSFERASE ; ligands: ACY ; X-RAY DIFFRACTION 2.05Å
e5wggA2[A:1-79] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Radical SAM domain protein ; ligands: CA ; X-RAY DIFFRACTION 2.050Å
e1qzzA1[A:10-101] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
aclacinomycin-10-hydroxylase ; X-RAY DIFFRACTION 2.1Å
e1xmxA2[A:161-247] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH
hypothetical protein VC1899 ; ligands: FMT ; X-RAY DIFFRACTION 2.1Å
see Frontiers in Genetics 5:102
e6gos11[1:12-90] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Microcin B17-processing protein McbB ; ligands: EDO ; X-RAY DIFFRACTION 2.100Å
e1lvaA3[A:511-574] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
SELENOCYSTEINE-SPECIFIC ELONGATION FACTOR ; X-RAY DIFFRACTION 2.12Å
e5z2iB1[B:29-120] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Dictyostelium discoideum mitochondrial calcium uniporter ; X-RAY DIFFRACTION 2.14Å
e6ec8A2[A:243-360] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Lantibiotic dehydratase domain protein ; X-RAY DIFFRACTION 2.148Å
e2xvcA1[A:204-259] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
ESCRT-III ; ligands: CD ; X-RAY DIFFRACTION 2.15Å
e3h35A1[A:31-174] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH
uncharacterized protein ABO_0056 ; ligands: EDO ; X-RAY DIFFRACTION 2.150Å
e6btcA1[A:1-85] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
LP1413 - SCCmec type IV-encoded DNA binding protein ; X-RAY DIFFRACTION 2.177Å
e5z08C1[C:161-191,C:258-328] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Cenp-K ; X-RAY DIFFRACTION 2.199Å
e2co5A1[A:5-93] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
VIRAL PROTEIN F93 ; X-RAY DIFFRACTION 2.20Å
e5u1eA1[A:1-79] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Putative gentamicin methyltransferase ; X-RAY DIFFRACTION 2.213Å
e4d7kF1[F:11-98] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
SAM-DEPENDENT METHYLTRANSFERASES ; X-RAY DIFFRACTION 2.22Å
e5xfrA5[A:261-357] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Metal-response element-binding transcription factor 2 ; X-RAY DIFFRACTION 2.25Å
e1x19A4[A:-11-96] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
CrtF-related protein ; ligands: SO4 ; X-RAY DIFFRACTION 2.27Å
e5uujA2[A:89-196] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
AlkZ ; X-RAY DIFFRACTION 2.299Å
e4i99D2[D:144-212] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Putative uncharacterized protein ; X-RAY DIFFRACTION 2.3Å
e5dfnB1[B:18-129] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Telomerase associated protein p45 ; X-RAY DIFFRACTION 2.380Å
e5dfnB2[B:130-213] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Telomerase associated protein p45 ; X-RAY DIFFRACTION 2.380Å
e6b39A2[A:87-227] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
AprA Methyltransferase 1 ; ligands: SO4 ; X-RAY DIFFRACTION 2.390Å
e1w5sA1[A:300-409] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
ORIGIN RECOGNITION COMPLEX SUBUNIT 2 ORC2 ; X-RAY DIFFRACTION 2.4Å
e4trbA1[A:2-9,A:146-210] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Purine phosphoribosyltransferase (GpT-1) ; X-RAY DIFFRACTION 2.4Å
e4a4zA3[A:801-830,A:1087-1123] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
ANTIVIRAL HELICASE SKI2 ; ligands: EDO ; X-RAY DIFFRACTION 2.40Å
e6hlkA1[A:35-165] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Redirecting phage packaging protein C (RppC) ; X-RAY DIFFRACTION 2.4158Å
e5oqdC2[C:574-693] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Polycomb protein Pcl ; ligands: EDO,PO4 ; X-RAY DIFFRACTION 2.447Å
e5v1qB1[B:1-101] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Radical SAM ; X-RAY DIFFRACTION 2.5Å
e6s2pN1[N:392-487] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
NRC1 ; ligands: ADP ; X-RAY DIFFRACTION 2.5Å
e5do0B2[B:335-446] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
protein lysine methyltransferase 1 ; X-RAY DIFFRACTION 2.600Å
e4k51B3[B:415-475] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Eukaryotic translation initiation factor 3 subunit A ; X-RAY DIFFRACTION 2.65Å
e4f91B21[B:888-993] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
U5 small nuclear ribonucleoprotein 200 kDa helicase ; X-RAY DIFFRACTION 2.69Å
e4lctA1[A:325-349] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
COP9 signalosome complex subunit 1 ; X-RAY DIFFRACTION 2.7Å
e4lctC2[C:325-352] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
COP9 signalosome complex subunit 1 ; X-RAY DIFFRACTION 2.7Å
e5me9A2[A:299-432] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Cell division cycle protein CDT1 ; ligands: GOL,SO4 ; X-RAY DIFFRACTION 2.7Å
e6f3hA3[A:829-896] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Exoribonuclease II, mitochondrial ; X-RAY DIFFRACTION 2.7Å
e6f3hB2[B:189-319] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Exoribonuclease II, mitochondrial ; X-RAY DIFFRACTION 2.7Å
e5lstA3[A:837-857,A:883-941,A:1033-1061] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
ATP-dependent DNA helicase Q4 ; ligands: ZN ; X-RAY DIFFRACTION 2.75Å
e5lstA4[A:942-1032] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
ATP-dependent DNA helicase Q4 ; X-RAY DIFFRACTION 2.75Å
e5dcaA12[A:1742-1857] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Pre-mRNA-splicing helicase BRR2 ; X-RAY DIFFRACTION 2.8Å
e5dcaA6[A:908-1009] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Pre-mRNA-splicing helicase BRR2 ; X-RAY DIFFRACTION 2.8Å
e5wtnA1[A:3-152] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Replication initiation and membrane attachment protein ; X-RAY DIFFRACTION 2.8Å
e3h5aA4[A:1-109] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
MccB protein ; X-RAY DIFFRACTION 2.800Å
e2xgjA3[A:578-608,A:874-910] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
ATP-DEPENDENT RNA HELICASE DOB1 ; X-RAY DIFFRACTION 2.9Å
e3t5vB2[B:338-455] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Nuclear mRNA export protein THP1 ; X-RAY DIFFRACTION 2.9Å
e4wd9A1[A:121-233] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Nisin biosynthesis protein NisB ; X-RAY DIFFRACTION 2.9Å
circular permutation
e2p6rA1[A:404-488] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
afUHEL308 HELICASE ; X-RAY DIFFRACTION 3.0Å
e5dooB2[B:307-418] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
protein lysine methyltransferase 2 ; X-RAY DIFFRACTION 3.100Å
e4a12B2[B:4-51] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
TRANSCRIPTION FACTOR FAPR ; X-RAY DIFFRACTION 3.15Å
e6mfvA3[A:328-392] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
tetratricopeptide repeat sensor PH0952 ; ligands: ADP ; X-RAY DIFFRACTION 3.40Å
e1u5tB2[B:490-564] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Defective in vacuolar protein sorting; Vps36p ; X-RAY DIFFRACTION 3.6Å
e1w7pD2[D:490-566] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
VPS36P, YLR417W ; X-RAY DIFFRACTION 3.600Å
e4bujA3[A:799-1121] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
ANTIVIRAL HELICASE SKI2 ; X-RAY DIFFRACTION 3.70Å
e2le8B1[B:380-408] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
DNA replication factor Cdt1 ; SOLUTION NMR
e2ly1A1[A:256-341] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH
TUDOR DOMAIN-CONTAINING PROTEIN 7 ; SOLUTION NMR
e2ly1A2[A:342-433] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH
TUDOR DOMAIN-CONTAINING PROTEIN 7 ; SOLUTION NMR
e4ui9N4[N:660-730] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
ANAPHASE-PROMOTING COMPLEX SUBUNIT 2 ; ELECTRON MICROSCOPY
e5lgmA1[A:16-84] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Fusion protein 5.5/5.7 ; SOLUTION NMR
e5mc6h7[h:1034-1120] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Antiviral helicase SKI2 ; ELECTRON MICROSCOPY
e6gw7A1[A:13-57] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
DNA protecting protein DprA ; SOLUTION NMR
e6o9lR3[R:210-242] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
Transcription initiation factor IIE subunit beta ; ELECTRON MICROSCOPY
e6v93G1[G:1-117] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
DNA polymerase delta subunit 3 ; ELECTRON MICROSCOPY
e6wgc31[3:892-960] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI
DNA replication licensing factor MCM3 ; ELECTRON MICROSCOPY
lacks the N-terminal helix, circularly permuted wing
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
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