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

X: Snake toxin-like

X: Defensin-like

X: Rattusin, a novel defensin with intermolecular disulfides

X: Epidermal patterning factor-like protein 9

X: BPTI-like

X: Cystine-knot cytokines

X: beta-beta-alpha zinc fingers

X: Inhibitor of apoptosis (IAP) repeat

X: Viral leader polypeptide zinc finger

X: Zinc finger domain in TOPLESS related protein 2 (TPR2)

X: E6 C-terminal domain-like

X: Zinc finger domain in intron-associated endonuclease 1

X: I-superfamily conotoxin r11a

X: omega toxin-like

H: omega toxin-related

T: omega toxin-related

T: Plant lectins/antimicrobial peptides

T: Colipase-like

T: Cyclotides

linked to omega toxin-like with lower scores

T: Scorpion toxin-like

F: Toxin_3

PF00537 CL0054

F: Toxin_2

PF00451 CL0054

Representatives:

e1r1gA1[A:1-31] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Neurotoxin BmK37 ; X-RAY DIFFRACTION 1.72Å

e1agtA1[A:1-38] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed,

AGITOXIN 2 ; SOLUTION NMR

e1bahA1[A:1-37] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

CHARYBDOTOXIN ; SOLUTION NMR

e1j5jA1[A:1-36] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

BeKm-1 toxin ; SOLUTION NMR

e1m2sA1[A:1-37] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Toxin BmTX3 ; SOLUTION NMR

e2kp0A1[A:1-33] Image Pymol Jmol Links: PDB, SCOP, CATH

nasonin-1M ; SOLUTION NMR

e1c56A1[A:3-39] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

BUTANTOXIN ; SOLUTION NMR

e1jlzA1[A:1-23] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Tityustoxin alpha-KTx ; SOLUTION NMR

e1bigA1[A:1-36] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

TOXIN BMTX1 ; SOLUTION NMR

e1lglA1[A:1-36] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

BeKm-1 toxin ; SOLUTION NMR

e1q2kA1[A:1-31] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Neurotoxin BmK37 ; SOLUTION NMR

e1r1gB1[B:1-31] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Neurotoxin BmK37 ; X-RAY DIFFRACTION 1.72Å

e1lirA1[A:1-37] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

LQ2 ; SOLUTION NMR

e2bmtA1[A:1-37] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

TOXIN BMTX2 ; SOLUTION NMR

e2crdA1[A:1-37] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

CHARYBDOTOXIN ; SOLUTION NMR

e1sxmA1[A:1-39] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

NOXIUSTOXIN ; SOLUTION NMR

e1mtxA1[A:1-39] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

MARGATOXIN ; SOLUTION NMR

e1scoA1[A:1-38] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

SCORPION TOXIN OSK1 ; SOLUTION NMR

e1xswA1[A:1-38] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Kaliotoxin 1 ; SOLID-STATE NMR

e1hlyA1[A:1-39] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

HONGOTOXIN 1 ; SOLUTION NMR

e1bktA1[A:1-37] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

BMKTX ; SOLUTION NMR

e1tskA1[A:1-35] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

TS KAPA ; SOLUTION NMR

e1ktxA1[A:1-37] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

KALIOTOXIN ; SOLUTION NMR

e1hp2A1[A:1-37] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

TITYUSTOXIN K ALPHA ; SOLUTION NMR

e2ktxA1[A:1-38] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed,

KALIOTOXIN ; SOLUTION NMR

e2uvsA1[A:1-38] Image Pymol Jmol Links: PDB, SCOP, CATH

POTASSIUM CHANNEL TOXIN ALPHA-KTX 3.1 ; SOLID-STATE NMR

e1wmtA1[A:2-39] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

IsTX ; SOLUTION NMR

e2ptaA1[A:4-38] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PANDINUS TOXIN K-ALPHA ; SOLUTION NMR

e1c49A1[A:4-38] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

TOXIN K-BETA ; SOLUTION NMR

e1wpdA1[A:1-34] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Potassium channel toxin alpha-KTx 6.2,Potassium channel toxin alpha-KTx 6.3 ; SOLUTION NMR

e3odvA1[A:1-38] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

POTASSIUM CHANNEL TOXIN ALPHA-KTX 3.1 ; ligands: CIT,TFA ; X-RAY DIFFRACTION 0.95Å

e3e8yX1[X:2-31] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

POTASSIUM CHANNEL TOXIN ALPHA-KTX 19.1 ; ligands: CL ; X-RAY DIFFRACTION 1.1Å

e2axkA1[A:1-38] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

discrepin ; SOLUTION NMR

e2ck4A1[A:1-38] Image Pymol Jmol Links: PDB, SCOP, CATH

POTASSIUM CHANNEL TOXIN ALPHA-KTX 3.7 ; SOLUTION NMR

e2k4uA1[A:1-37] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Potassium channel toxin alpha-KTx 3.6 ; SOLUTION NMR

e1wz5A1[A:1-35] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Potassium channel blocking toxin 1 ; SOLUTION NMR

e1y2pA1[A:1-34] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Neurotoxin HsTX1 ; SOLUTION NMR

e2ck5A1[A:1-31] Image Pymol Jmol Links: PDB, SCOP, CATH

POTASSIUM CHANNEL TOXIN ALPHA-KTX 3.7 ; SOLUTION NMR

e3odvB1[B:1-38] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

POTASSIUM CHANNEL TOXIN ALPHA-KTX 3.1 ; ligands: CIT,TFA ; X-RAY DIFFRACTION 0.95Å

e1quzA1[A:1-35] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

HSTX1 TOXIN ; SOLUTION NMR

e1cmrA1[A:1-31] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

CHARYBDOTOXIN, ALPHA CHIMERA ; SOLUTION NMR

e2a9hE1[E:801-837] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

charybdotoxin ; SOLUTION NMR

e2k9oA1[A:1-36] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

VM24 SCORPION TOXIN ; SOLUTION NMR

e2kirA1[A:1-34] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Designer toxin ; SOLUTION NMR

e1pjvA1[A:1-31] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Cobatoxin 1 ; SOLUTION NMR

e4jtaY1[Y:1-37] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Potassium channel toxin alpha-KTx 1.1 ; X-RAY DIFFRACTION 2.500Å

e4jtcY1[Y:1-37] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Potassium channel toxin alpha-KTx 1.1 ; ligands: CS ; X-RAY DIFFRACTION 2.560Å

e4jtdY1[Y:1-37] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Potassium channel toxin alpha-KTx 1.1 ; X-RAY DIFFRACTION 2.540Å

e1c55A2[A:1-40] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

BUTANTOXIN ; SOLUTION NMR

e2rtzA1[A:1-29] Image Pymol Jmol Links: PDB, SCOP, CATH

Potassium channel blocker MarkTX-7 ; SOLUTION NMR

e2mlaA1[A:1-37] Image Pymol Jmol Links: PDB, SCOP, CATH

; SOLUTION NMR

e2mldA1[A:1-37] Image Pymol Jmol Links: PDB, SCOP, CATH

; SOLUTION NMR

e6avcA1[A:2-38] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Potassium channel toxin alpha-KTx 1.5 ; X-RAY DIFFRACTION 1.88Å

e6atlA1[A:-1-35] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Potassium channel toxin alpha-KTx 4.2 ; ligands: CIT,SO4 ; X-RAY DIFFRACTION 1.80Å

e6atnA1[A:-1-37] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Potassium channel toxin alpha-KTx 4.5 ; X-RAY DIFFRACTION 1.76Å

e6au7B1[B:-1-36] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Potassium channel toxin gamma-KTx 2.2 ; ligands: GOL ; X-RAY DIFFRACTION 1.90Å

e6au7C1[C:-1-36] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Potassium channel toxin gamma-KTx 2.2 ; ligands: GOL,SO4 ; X-RAY DIFFRACTION 1.90Å

e6au7D1[D:-1-36] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Potassium channel toxin gamma-KTx 2.2 ; ligands: SO4 ; X-RAY DIFFRACTION 1.90Å

e6aupA1[A:-1-36] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI