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: barrettide A

X: Leech antihemostatic protein

X: Plant proteinase inhibitors

X: Embryo surrounding factor (ESF) peptides

X: Type AII lantibiotic bovicin HJ50

X: PSCD domain of pleuralin-1

X: Sea anemone toxin k-like

X: Trefoil/Plexin domain-like

X: Variant surface glycoprotein MITAT 1.2, VSG 221, C-terminal domain

X: PMP inhibitors

X: Ectatomin/elicitin

X: Bowman-Birk inhibitor, BBI-like

X: DnaJ/Hsp40 cysteine-rich domain

X: P-domain of calnexin/calreticulin

X: Thyroglobulin type-1 domain

X: Shisa 3 N-terminal domain

X: TAZ domain

X: Zn-binding domain in DNA polymerase III subunits

X: N-terminal domain of helicase-loading protein DnaI

X: Tim10/DDP

X: Sec-C motif

X: Vanabin-like

X: Crambin-like

X: Blood coagulation inhibitor (disintegrin)

X: Insulin-like

X: Cellophane-induced 1 (cin1) repeats

X: Conotoxin im17a

X: Conotoxin F14

X: con-ikot-ikot toxin

X: TB module/8-cys domain

X: Phospholipase A2, PLA2

X: Zn2/Cys6 DNA-binding domain

X: HIPIP (high potential iron protein)

X: Ezh2 MCSS domain

X: C-P lyase subunit PhnJ C-terminal Zn-binding domain

X: Pre-mRNA-splicing factor BUD31

X: Protein-only RNase P Zn-binding domain

X: RelA zinc-finger domain

X: Rubredoxin-like

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

X: Zinc-binding domain in Junin virus envelope glycoprotein

X: FusB family Zn-binding domain

X: Zinc finger domain in hydrogenase maturation protein HypF

X: Ribosomal protein L36

X: Btk/CHORD zinc fingers

X: CHY zinc finger

X: Trm112p-like

X: beta-barrel domain in Capz

X: Zinc hairpin stack

X: HSP33 redox switch-like

X: Coronavirus NSP10-like

X: T-antigen specific domain-like

X: Late competence protein ComFB

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: Zinc-binding domain of DENR

X: E3 ligase HOIP C-terminal domain

X: Avirulence protein AvrP123

X: E7 C-terminal domain-like

X: C4H2C2-type zinc finger

X: Glucocorticoid receptor-like

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

X: CRISPR RNA silencing complex Cmr2 subunit Zn-binding domain

X: Zn3Cys9 preSET domain-related

X: Metallothionein

X: Ribosomal protein bL28-related

X: Ribosomal protein L31p

X: His-Me finger endonucleases

X: CRISPR-associated endonuclease Cpf1 nuclease domain

X: CRISPR-associated endonuclease C2c1 C-terminal domain

X: Kazal-type serine protease inhibitors-like

X: Kringle-like

H: Kringle-like

T: Kringle-like

F: Kringle

PF00051 CL0602

F: fn2

PF00040 CL0602

Representatives:

e1h8pA1[A:22-67] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

SEMINAL PLASMA PROTEIN PDC-109 ; ligands: PC ; X-RAY DIFFRACTION 1.820Å

e8hbcA4[A:157-210] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Lymphocyte antigen 75 ; X-RAY DIFFRACTION 3.35Å

e8hbcB4[B:157-210] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Lymphocyte antigen 75 ; X-RAY DIFFRACTION 3.35Å

e5e4kA2[A:175-229] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

C-type mannose receptor 2 ; ligands: PE5 ; X-RAY DIFFRACTION 2.58Å

e5ew6A1[A:174-229] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

C-type mannose receptor 2 ; ligands: 1PE ; X-RAY DIFFRACTION 2.29Å

e1h8pB1[B:68-109] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

SEMINAL PLASMA PROTEIN PDC-109 ; ligands: PC ; X-RAY DIFFRACTION 1.820Å

e1h8pB2[B:22-67] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

SEMINAL PLASMA PROTEIN PDC-109 ; ligands: PC ; X-RAY DIFFRACTION 1.820Å

e1pdcA1[A:-2-42] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

SEMINAL FLUID PROTEIN PDC-109 ; SOLUTION NMR

e1h8pA2[A:68-109] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

SEMINAL PLASMA PROTEIN PDC-109 ; ligands: PC ; X-RAY DIFFRACTION 1.820Å

e1eakD2[D:336-393] Image Pymol Jmol Links: PDB, SCOP, CATH

72 KDA TYPE IV COLLAGENASE ; X-RAY DIFFRACTION 2.650Å

e1eakB2[B:278-335] Image Pymol Jmol Links: PDB, SCOP, CATH

72 KDA TYPE IV COLLAGENASE ; ligands: SO4 ; X-RAY DIFFRACTION 2.650Å

e1e88A1[A:102-160] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

FIBRONECTIN ; ligands: NAG ; SOLUTION NMR

e1eakA2[A:336-393] Image Pymol Jmol Links: PDB, SCOP, CATH

72 KDA TYPE IV COLLAGENASE ; X-RAY DIFFRACTION 2.650Å

e1eakD3[D:278-335] Image Pymol Jmol Links: PDB, SCOP, CATH

72 KDA TYPE IV COLLAGENASE ; ligands: SO4 ; X-RAY DIFFRACTION 2.650Å

e1gxdB3[B:309-364] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

72 KDA TYPE IV COLLAGENASE ; X-RAY DIFFRACTION 3.100Å

e1l6jA3[A:332-390] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

MATRIX METALLOPROTEINASE-9 ; X-RAY DIFFRACTION 2.5Å

e1gxdB4[B:249-306] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

72 KDA TYPE IV COLLAGENASE ; ligands: SO4 ; X-RAY DIFFRACTION 3.100Å

e1eakC2[C:219-277] Image Pymol Jmol Links: PDB, SCOP, CATH

72 KDA TYPE IV COLLAGENASE ; X-RAY DIFFRACTION 2.650Å

e1e8bA1[A:102-160] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

FIBRONECTIN ; ligands: NAG ; SOLUTION NMR

e1gxdB5[B:190-248] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

72 KDA TYPE IV COLLAGENASE ; X-RAY DIFFRACTION 3.100Å

e1eakC3[C:278-335] Image Pymol Jmol Links: PDB, SCOP, CATH

72 KDA TYPE IV COLLAGENASE ; ligands: SO4 ; X-RAY DIFFRACTION 2.650Å

e1e8bA2[A:42-100] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

FIBRONECTIN ; SOLUTION NMR

e1eakD4[D:219-277] Image Pymol Jmol Links: PDB, SCOP, CATH

72 KDA TYPE IV COLLAGENASE ; X-RAY DIFFRACTION 2.650Å

e1eakC4[C:336-393] Image Pymol Jmol Links: PDB, SCOP, CATH

72 KDA TYPE IV COLLAGENASE ; X-RAY DIFFRACTION 2.650Å

e1eakA3[A:278-335] Image Pymol Jmol Links: PDB, SCOP, CATH

72 KDA TYPE IV COLLAGENASE ; ligands: SO4 ; X-RAY DIFFRACTION 2.650Å

e1l6jA4[A:275-331] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

MATRIX METALLOPROTEINASE-9 ; X-RAY DIFFRACTION 2.5Å

e1qo6A1[A:42-100] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

FIBRONECTIN ; SOLUTION NMR

e1ck7A3[A:219-277] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROTEIN (GELATINASE A) ; X-RAY DIFFRACTION 2.8Å

e1eakB3[B:336-393] Image Pymol Jmol Links: PDB, SCOP, CATH

72 KDA TYPE IV COLLAGENASE ; X-RAY DIFFRACTION 2.650Å

e1ck7A4[A:278-335] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROTEIN (GELATINASE A) ; ligands: SO4 ; X-RAY DIFFRACTION 2.8Å

e1eakA4[A:219-277] Image Pymol Jmol Links: PDB, SCOP, CATH

72 KDA TYPE IV COLLAGENASE ; X-RAY DIFFRACTION 2.650Å

e2fn2A1[A:1-59] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

FIBRONECTIN ; ligands: NAG ; SOLUTION NMR

e1eakB4[B:219-277] Image Pymol Jmol Links: PDB, SCOP, CATH

72 KDA TYPE IV COLLAGENASE ; ligands: SO4 ; X-RAY DIFFRACTION 2.650Å

e1e88A2[A:42-100] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

FIBRONECTIN ; SOLUTION NMR

e1ck7A5[A:336-393] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROTEIN (GELATINASE A) ; X-RAY DIFFRACTION 2.8Å

e2v5oA5[A:1895-1944] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

CATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR ; X-RAY DIFFRACTION 2.90Å

e1ks0A1[A:1-58] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Matrix Metalloproteinase 2 ; SOLUTION NMR

e1j7mA1[A:1-59] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

MATRIX METALLOPROTEINASE 2 ; SOLUTION NMR

e1cxwA1[A:1-59] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

HUMAN MATRIX METALLOPROTEINASE 2 ; SOLUTION NMR

e3m7pA1[A:405-464] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

FN1 PROTEIN ; ligands: NAG ; X-RAY DIFFRACTION 2.5Å

e3mqlA1[A:405-464] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

FIBRONECTIN 1 ; ligands: MPD,NAG ; X-RAY DIFFRACTION 3.0Å

e2v5pB7[B:1897-1944] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

CATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR ; X-RAY DIFFRACTION 4.10Å

e2v5pA6[A:1897-1945] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

CATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR ; X-RAY DIFFRACTION 4.10Å

e3m7pA19[A:347-404] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

FN1 PROTEIN ; ligands: 12P,ZN ; X-RAY DIFFRACTION 2.5Å

e3mqlA8[A:347-404] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

FIBRONECTIN 1 ; ligands: MRD ; X-RAY DIFFRACTION 3.0Å

e1gxdA1[A:188-248] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

72 KDA TYPE IV COLLAGENASE ; X-RAY DIFFRACTION 3.100Å

e1gxdA6[A:249-306] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

72 KDA TYPE IV COLLAGENASE ; ligands: SO4 ; X-RAY DIFFRACTION 3.100Å

e1gxdA2[A:307-364] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

72 KDA TYPE IV COLLAGENASE ; X-RAY DIFFRACTION 3.100Å

e5ao5A2[A:175-229] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

C-TYPE MANNOSE RECEPTOR 2 ; ligands: SO4 ; X-RAY DIFFRACTION 2.48Å

e5ao5B2[B:175-229] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

C-TYPE MANNOSE RECEPTOR 2 ; ligands: SO4 ; X-RAY DIFFRACTION 2.48Å

e5ao6A2[A:174-229] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

C-TYPE MANNOSE RECEPTOR 2 ; X-RAY DIFFRACTION 3.36Å

e5ao6B2[B:174-229] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

C-TYPE MANNOSE RECEPTOR 2 ; X-RAY DIFFRACTION 3.36Å

e5e4lA4[A:174-229] Image Pymol Jmol Links: PDB, SCOP, CATH

C-type mannose receptor 2 ; X-RAY DIFFRACTION 2.44Å

e5e4lB2[B:174-229] Image Pymol Jmol Links: PDB, SCOP, CATH

C-type mannose receptor 2 ; X-RAY DIFFRACTION 2.44Å

e5xtwC1[C:156-210] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI