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

X: C-type lectin-like

X: Noncollagenous (NC1) domain of collagen IV

X: RNase A-like

X: Procyclic specific surface antigen-2

X: Helicase Cch N-terminal domain

X: Suppressor of hydroxyurea sensitivity protein 2

X: Immune Mapped Protein 2 (IMP2)

X: USP8 interacting domain

X: PA1123-like

X: Type III R-M system modification subunit target recognition domain

X: Hemolysin II

X: Outer capsid protein VP2 body domain

X: Mitoribosomal protein mS22

X: Putative lipoprotein BA_2398

X: Head and neck region of the ectodomain of paramyxoviruses fusion glycoprotein

X: S2 subunit of coronavirus spike glycoprotein

X: nsP3 zinc-binding domain

X: Herpesvirus UL21 N-terminal domain

X: Cysteine proteinases-like

X: Late protein H7

X: Lmo1499 protein N-terminal domains

X: Lysozyme-like

X: spore cortex-lytic enzyme catalytic domain

X: Nigritoxin N-terminal domain

X: Nigritoxin C-terminal domain

X: ADP-ribosylation

X: Tic22

X: Ribosomal protein TL5/L25 C-terminal domain-like

X: Zinc finger FYVE domain-containing protein 9 C-terminal domain

X: Argininosuccinate synthetase-C

X: LCCL domain

X: Aromatic aminoacid monoxygenases, catalytic and oligomerization domains

X: Methionine synthase activation domain-like

X: Nitric oxide (NO) synthase oxygenase domain

X: Metal cation-transporting ATPase, ATP-binding domain

X: Fibrinogen C-terminal domain-like

X: Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain

X: LDH C-terminal domain-like

X: Diaminopimelate epimerase-like

X: Anchorless fibronectin/fibrinogen binding protein C-terminal domain

X: Yos9 dimerization domain

X: Peptide deformylase

X: YrdC/RibB

X: YbaK/ProRS associated domain

X: CoA-dependent acyltransferases

X: alpha/beta-Hammerhead/Barrel-sandwich hybrid

X: DNA mimic protein DMP12-like

X: Hypothetical protein HI1480

X: RuBisCo LSMT C-terminal, substrate-binding domain

X: 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain

X: Cell cycle regulatory proteins

X: Conserved core of transcriptional regulatory protein vp16

X: Nitrile hydratase alpha chain

X: Proguanylin

X: Rotavirus NSP2 fragment, N-terminal domain

X: VSV matrix protein

X: ssRNA bacteriophage MS2 maturation protein

X: YopH tyrosine phosphatase N-terminal domain

X: Hsp33 domain

X: Outer capsid protein sigma 3-related

X: mRNA triphosphatase CET1-related

X: Phosphoinositide phosphatase SAC1 N-terminal domain

X: ParB/Sulfiredoxin

X: Aha1/BPI domain-like

X: lantibiotic self-resistance lipoprotein MlbQ

X: RGC domain

X: Transcription factor NusA, N-terminal domain

X: N-terminal subdomain in DNA replication initiator (cdc21/cdc54)

X: N-terminal domain in beta subunit of DNA dependent RNA-polymerase

X: insertion domain in beta subunit of DNA dependent RNA-polymerase

X: barrel domain in beta subunit of DNA dependent RNA-polymerase

X: inserted a+b domain in yeast RNA polymerase beta subunit

X: C-terminal domain in beta subunit of DNA dependent RNA-polymerase

X: N-terminal domain in RNA-polymerase beta-prime subunit

X: Helical hairpin insertion in E. coli DNA-directed RNA polymerase beta subunit

X: first helical domain in RNA-polymerase beta-prime subunit

X: second helical domain in RNA-polymerase beta-prime subunit

X: helical domain in yeast RNA-polymerases

X: central helical domain in RNA-polymerase beta-prime subunit

X: Sandwich domain in replication terminator protein (Tus)

X: Insertion domain in replication terminator protein (Tus)

X: a+b domain in virulence-associated V antigen

X: Serpins

X: Ribonuclease P protein subunit p40

X: a+b domain in membrane penetration protein mu1

X: Inner layer core protein p3-related

X: Major inner capsid protein P1

X: L-A virus major coat protein-related

X: Major capsid protein VP5

X: MoeA domain II

X: BB1717-like

X: DNA methylase specificity domain

X: L,D-transpeptidase pre-catalytic domain-like

X: YbiA-like

X: ORC1-binding domain

X: BTG domain-like

X: DUSP, domain in ubiquitin-specific proteases

X: STIV B116-like

X: TBP-interacting protein C-terminal domain-like

X: N-terminal domain in viral ssDNA binding protein

X: first a+b domain in acetyl-CoA synthase

X: second a+b domain in acetyl-CoA synthase

X: insertion domain in bacteriophage phi29 DNA polymerase

X: linker domain in MalF N-terminal region

X: barrel domain in MalF N-terminal region

X: C-terminal a+b domain in Poly(A) polymerase catalytic subunit

X: Flu NP-like

X: Domain II in tail sheath protein Gp18

X: Flagellar protein FlgA N-terminal domain-like

X: N0 domain in phage tail proteins and secretins-like

X: C-terminal insertion domain in phage tail proteins

X: Hypothetical protein TA0956

X: Necrosis and ethylene-inducing peptide 1-like proteins

X: Envelope glycoprotein GP1

X: Arenavirus glycoprotein GP2

X: Uncharacterized protein yutD

X: Myosin VI cargo binding domain

X: MESD

X: gH main domain

X: bacteriophage phiKZ gp29PR

X: Regulatory domain of isocitrate dehydrogenase kinase/phosphatase

X: Baseplate wedge protein gp7 domain II

X: IBV Nsp2a

X: Reovirus guanylyltransferase (GTase)

X: Reovirus turret protein bridge domain

X: LidA

X: Adenine deaminase 2 C-terminal domain

X: Insertion domain in vaccinia virus scaffolding protein D13

X: Insertion domain in O-GlcNAc transferase

X: Insertion domain in Adenovirus penton base protein

X: Membrane-associated protein VP24

X: Envelope glycoprotein GP1

X: DUF2666 family proteins

X: Primosome assembly protein PriA 3' DNA-binding domain

X: P9-1

X: ArdA

X: RapA C-terminal domain

X: Polymerase acidic protein

X: Mediator of RNA polymerase II transcription submodule Med7N/31

X: Mediator co-activator domain 1 of Gal11/med15

X: Mediator of RNA polymerase II transcription subunit 11

X: Mediator of RNA polymerase II transcription subunit 22

X: Mediator of RNA polymerase II transcription subunit 8

X: Mediator of RNA polymerase II transcription subunit 17

X: Cascade subunit Csa5

X: Cas8-like

X: Scaffolding protein GPB

X: Capsid protein

X: RNAi polymerase N-terminal domain

X: Tomato mosaic virus helicase N-terminal domain

X: Oncogenic effector CagA meander beta sheet domain

X: Tetrahydrodipicolinate N-succinyletransferase N-terminal domain

X: Transcription factor tau 60 kDa subunit

X: hypothetical protein BF0379 C-terminal domain

X: SRCR-like

X: conserved hypothetical protein MTH0776

X: C-terminal domain of BipA

X: C-terminal domain of cytoplasmic dynein heavy chain

X: Protein kinase/SAICAR synthase/ATP-grasp

H: Protein kinase/SAICAR synthase/ATP-grasp

T: Protein kinase

F: Haspin_kinase

F: ,B

F: ,Pkinase_C

F: ABC1

F: Kdo

F: Kinase-like

F: ,TGF_beta_GS

F: Act-Frag_cataly

F: HipA_C,Couple_hipA

F: CotH

F: Fam20C

F: APH

Representatives:

e2ppqA1[A:5-320] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

HOMOSERINE KINASE ; ligands: MG,PO4 ; X-RAY DIFFRACTION 2.0Å

e2pulA1[A:5-396] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Methylthioribose kinase ; ligands: ACP,CPS,MG ; X-RAY DIFFRACTION 2.0Å

e1nd4A1[A:10-264] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Aminoglycoside 3'-phosphotransferase ; ligands: ACT,KAN,MG,NA ; X-RAY DIFFRACTION 2.1Å

e1j7lA1[A:2-264] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

AMINOGLYCOSIDE 3'-PHOSPHOTRANSFERASE ; ligands: ADP,MG ; X-RAY DIFFRACTION 2.2Å

e6iy9A1[A:3-327] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Hygromycin-B 7''-O-kinase ; ligands: FLC,HY0,NHE ; X-RAY DIFFRACTION 2.4Å

e1zylA1[A:4-328] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Hypothetical protein yihE ; X-RAY DIFFRACTION 2.800Å

e4uw0A1[A:223-459] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

WBDD ; X-RAY DIFFRACTION 3.87Å

e4azvA3[A:208-473] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

WBDD ; ligands: SO4 ; X-RAY DIFFRACTION 3.29Å

e4bwkB3[B:235-515] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN-3 ; ligands: AGS ; X-RAY DIFFRACTION 3.3Å

e4bwkA3[A:235-514] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN-3 ; ligands: AGS ; X-RAY DIFFRACTION 3.3Å

e4azwA5[A:229-398,A:418-449] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

WBDD ; ligands: ATP,MG ; X-RAY DIFFRACTION 2.47Å

e4czyB2[B:234-501] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN3 ; ligands: ANP,MG ; X-RAY DIFFRACTION 3.4Å

e4azsA5[A:209-473] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

METHYLTRANSFERASE WBDD ; ligands: AMP,SO4 ; X-RAY DIFFRACTION 2.15Å

e4ax8A5[A:209-473] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

WBDD ; ligands: ADP,SO4 ; X-RAY DIFFRACTION 3.0Å

e4q8jF1[F:228-535] Image Pymol Jmol Links: PDB, SCOP, CATH Obsolete PDB

e4aztA1[A:209-471] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

METHYLTRANSFERASE WBDD ; ligands: LY2,SO4 ; X-RAY DIFFRACTION 2.34Å

e4q8jI2[I:229-533] Image Pymol Jmol Links: PDB, SCOP, CATH Obsolete PDB

e4bwxA1[A:234-515] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN-3 ; ligands: AGS,MG ; X-RAY DIFFRACTION 2.85Å

e4bwxB2[B:234-515] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN-3 ; ligands: AGS,MG ; X-RAY DIFFRACTION 2.85Å

e3otvD2[D:16-263] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE CONSERVED TRANSMEMBRANE PROTEIN ; X-RAY DIFFRACTION 3.094Å

e3otvA2[A:16-269] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE CONSERVED TRANSMEMBRANE PROTEIN ; X-RAY DIFFRACTION 3.094Å

e3uqcA2[A:16-261] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE CONSERVED TRANSMEMBRANE PROTEIN ; X-RAY DIFFRACTION 2.256Å

e3uqcD2[D:15-263] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE CONSERVED TRANSMEMBRANE PROTEIN ; X-RAY DIFFRACTION 2.256Å

e3uqcC2[C:13-262] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE CONSERVED TRANSMEMBRANE PROTEIN ; X-RAY DIFFRACTION 2.256Å

e3oukA2[A:17-264] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE CONSERVED TRANSMEMBRANE PROTEIN ; X-RAY DIFFRACTION 3.4Å

e3uqcB2[B:18-261] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE CONSERVED TRANSMEMBRANE PROTEIN ; ligands: SIN ; X-RAY DIFFRACTION 2.256Å

e3otvB2[B:18-261] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE CONSERVED TRANSMEMBRANE PROTEIN ; X-RAY DIFFRACTION 3.094Å

e3otvC2[C:13-269] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE CONSERVED TRANSMEMBRANE PROTEIN ; X-RAY DIFFRACTION 3.094Å

e4cyiA1[A:215-485] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI