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MolNFT v1 · #28019 · protein

Crystal structure of aa-X-bp-II, a snake venom protein with the activity of binding to coagulation factor X from agkistrodon acutus

1Y17 · Anticoagulant protein a: “Crystal structure of aa-X-bp-II, a snake venom protein with the activity of binding to coagulation factor X…”. X-ray diffraction, 1 ligand (CA). MolNFT v1 #28019 on GenesisL1: 3D structure, binding sites…

PDB
1Y17
Type
protein
Length
252 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Anticoagulant protein a; Anticoagulant protein-B
UniProt
Q9DEF9, Q9DEF8
Ligands
CA

Structure

x-ray diffraction · 2 distinct chains · 22% helix, 33% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AAnticoagulant protein aprotein12924% helix, 30% strandQ9DEF9
BAnticoagulant protein-Bprotein12320% helix, 37% strandQ9DEF8

Ligands and binding sites

  • CA · Calcium ion · metal · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Interfaces

1 interface between chains.

  • A–B · 1963 Ų buried · 26 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide (disulfide).

Compared structures

  • 1Y17 · crystal structure of Aa-X-bp-II, a snake venom protein with the activity of binding to… · the same entry in another collection · chain A against A, TM-score 1.00
  • Q9DEF9 · AlphaFold monomer V2.0 prediction for snaclec anticoagulant protein subunit a (Q9DEF9) · a predicted model of the same protein · chain A against A, TM-score 0.93
  • Q9DEF8 · AlphaFold monomer V2.0 prediction for snaclec anticoagulant protein subunit B (Q9DEF8) · a predicted model of the same protein · chain B against A, TM-score 0.92

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