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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

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

X: Rubredoxin-like

binds one zinc with two CxxC motifs on two beta-hairpins

H: Rubredoxin-related
T: Rubredoxin-related
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.

Representatives:

e1q1aA1[A:137-181] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

HST2 PROTEIN ; ligands: OAD,ZN ; X-RAY DIFFRACTION 1.5Å

e5a3aA2[A:139-191] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

SIR2 FAMILY PROTEIN ; ligands: EDO,GLY,ZN ; X-RAY DIFFRACTION 1.54Å

e5oj7A2[A:162-230] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

NAD-dependent protein deacylase ; ligands: EDO,ZN ; X-RAY DIFFRACTION 1.58Å

e5aunA1[A:69-123] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Probable hydrogenase nickel incorporation protein HypA ; ligands: NI,URE,ZN ; X-RAY DIFFRACTION 1.630Å

e1pfvA4[A:122-140,A:171-189] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

METHIONYL-TRNA SYNTHETASE ; X-RAY DIFFRACTION 1.7Å

e2gaiB5[B:550-601] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA TOPOISOMERASE I ; X-RAY DIFFRACTION 1.7Å

e4me3A3[A:133-187] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA replication licensing factor MCM related protein ; ligands: ZN ; X-RAY DIFFRACTION 1.794Å

e2xb4A1[A:125-161] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

ADENYLATE KINASE ; ligands: SRT,ZN ; X-RAY DIFFRACTION 1.8Å

e2b4yA1[A:160-220] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

NAD-DEPENDENT DEACETYLASE SIRTUIN-5 ; ligands: ZN ; X-RAY DIFFRACTION 1.9Å

e5urbA3[A:115-137,A:168-186] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

Methionine--tRNA ligase ; ligands: EDO,MET,NO3 ; X-RAY DIFFRACTION 1.900Å

e1s5pA1[A:149-187] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

NAD-DEPENDENT DEACETYLASE ; ligands: ZN ; X-RAY DIFFRACTION 1.96Å

e1wkbA1[A:513-582] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Leucyl-tRNA synthetase ; X-RAY DIFFRACTION 2.05Å

e3ziuA3[A:260-318] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

LEUCYL-TRNA SYNTHETASE ; ligands: GOL ; X-RAY DIFFRACTION 2.07Å

e5ijlA3[A:728-781] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA polymerase II large subunit ; ligands: ZN ; X-RAY DIFFRACTION 2.19Å

e7ae5f1[f:603-639] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

Protein ShdD ; ligands: ZN ; X-RAY DIFFRACTION 2.19Å

e3zg6A3[A:133-183] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-6 ; ligands: ZN ; X-RAY DIFFRACTION 2.2Å

e1e5xA1[A:10-130] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

THREONINE SYNTHASE ; X-RAY DIFFRACTION 2.25Å

e5wgrA3[A:586-666] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Flavin-dependent halogenase ; ligands: PM7,SO4,ZN ; X-RAY DIFFRACTION 2.362Å

e1s0uA5[A:83-110] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Translation initiation factor 2 gamma subunit ; ligands: ZN ; X-RAY DIFFRACTION 2.4Å

e3f2bA6[A:915-955] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed DNA polymerase III alpha chain ; ligands: ZN ; X-RAY DIFFRACTION 2.400Å

e1ileA2[A:451-514] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

ISOLEUCYL-TRNA SYNTHETASE ; ligands: ZN ; X-RAY DIFFRACTION 2.5Å

e3u50C2[C:553-582] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Telomerase-associated protein 82 ; ligands: ZN ; X-RAY DIFFRACTION 2.500Å

e5zb8A2[A:247-277] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PfuEndoQ ; ligands: ZN ; X-RAY DIFFRACTION 2.500Å

e4pofA3[A:131-180] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Cell division control protein 21 ; ligands: ZN ; X-RAY DIFFRACTION 2.648Å

e4nl4H5[H:429-442,H:472-488] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Primosome assembly protein PriA ; ligands: ZN ; X-RAY DIFFRACTION 2.65Å

e2vl6B4[B:136-190] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

MINICHROMOSOME MAINTENANCE PROTEIN MCM ; ligands: ZN ; X-RAY DIFFRACTION 2.8Å

e1ivsA7[A:407-452] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

VALYL-TRNA SYNTHETASE ; X-RAY DIFFRACTION 2.9Å

e4iaoA2[A:366-442] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

NAD-dependent histone deacetylase SIR2 ; ligands: ZN ; X-RAY DIFFRACTION 2.90Å

e4rulA1[A:590-636] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA topoisomerase 1 ; ligands: ZN ; X-RAY DIFFRACTION 2.90Å

e2ahoA4[A:55-87] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Translation initiation factor 2 gamma subunit ; ligands: ZN ; X-RAY DIFFRACTION 3.0Å

e1ltlA3[A:124-172] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA replication initiator (Cdc21/Cdc54) ; ligands: ZN ; X-RAY DIFFRACTION 3.000Å

e4ddtA3[A:619-645] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Reverse gyrase ; ligands: ZN ; X-RAY DIFFRACTION 3.20Å

e1zt2A4[A:111-140] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA PRIMASE SMALL SUBUNIT ; ligands: SO4,ZN ; X-RAY DIFFRACTION 3.33Å

e1zakA1[A:128-158] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

ADENYLATE KINASE ; ligands: AP5 ; X-RAY DIFFRACTION 3.5Å

e4bbsL1[L:1-44] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4 ; ligands: ZN ; X-RAY DIFFRACTION 3.6Å

e4a3iL1[L:1-46] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4 ; ligands: ZN ; X-RAY DIFFRACTION 3.80Å

e1m2kA1[A:118-156] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Silent Information Regulator 2 ; ligands: ZN ; X-RAY DIFFRACTION

e1q5wA1[A:1-31] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

homolog of yeast nuclear protein localization 4 ; ligands: ZN ; SOLUTION NMR

e1wz2A2[A:175-205,A:443-509] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

Leucyl-tRNA synthetase ; X-RAY DIFFRACTION

e2gmgA3[A:66-99] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

HYPOTHETICAL PROTEIN PF0610 ; SOLUTION NMR

e3bbo21[2:1-57] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH Obsolete PDB

e3j81k3[k:146-187] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

eIF2 gamma ; ELECTRON MICROSCOPY

e3ja833[3:195-251] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Minichromosome Maintenance 3 ; ELECTRON MICROSCOPY

e3ja851[5:175-211,5:235-251] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Minichromosome Maintenance 5 ; ELECTRON MICROSCOPY

e3ja874[7:254-308] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Minichromosome Maintenance 7 ; ELECTRON MICROSCOPY

e3jc623[2:333-383] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA replication licensing factor MCM2 ; ELECTRON MICROSCOPY

e5oqj42[4:286-323] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RNA polymerase II transcription factor B subunit 4 ; ligands: ZN ; ELECTRON MICROSCOPY

e5oqj63[6:308-374] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Suppressor of stem-loop protein 1 ; ligands: ZN ; ELECTRON MICROSCOPY

e6hivBh1[Bh:2-92] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

mL100 ; ligands: SER,ZN ; ELECTRON MICROSCOPY

e6kf4G2[G:87-169] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Transcription factor E ; ligands: ZN ; ELECTRON MICROSCOPY

e6n8mY1[Y:225-352] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Tyrosine-protein phosphatase YVH1 ; ELECTRON MICROSCOPY

e6nmiE2[E:239-316] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

General transcription factor IIH subunit 2, p44 ; ligands: ZN ; ELECTRON MICROSCOPY

e6raw53[5:159-164,5:186-217] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA replication licensing factor Mcm5 ; ELECTRON MICROSCOPY

e6rax51[5:159-217] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA replication licensing factor Mcm5 ; ELECTRON MICROSCOPY

e6xtx53[5:164-222] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA replication licensing factor MCM5 ; ligands: ZN ; ELECTRON MICROSCOPY

T: Hypothetical protein Ta0289-C

insertion in the CxxC motif

X: RING/U-box-like

binds two zincs. one in the same way as rubredoxin, probably related to rubredoxin. the other in a similar way as glucocorticoid receptor

X: Glucocorticoid receptor-like

binds zinc with one beta-hairpin and one helix, the helix binds DNA

extended segmentsextended, non-globular segments, frequently bind to other proteins to form complexes