MolNFT v1 · #10341 · protein
Crystal structure of the complex between the coagulation factor X binding protein from snake venom and the gla domain of factor X
1IOD: “Crystal structure of the complex between the coagulation factor X binding protein from snake venom and the…”. X-ray diffraction, 1 ligand (CA), 2 pockets (best druggability 0.70). MolNFT v1 #10341 on GenesisL1: 3D structure, binding…
- PDB
- 1IOD
- Type
- protein
- Length
- 296 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor X binding protein; Coagulation factor X gla domain
- EC
- 3.4.21.6
- UniProt
- P00743
- Ligands
- CA
- Pockets
- 2 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coagulation factor X binding protein | protein | 129 | 22% helix, 29% strand | — |
| B | Coagulation factor X binding protein | protein | 123 | 21% helix, 36% strand | — |
| G | Coagulation factor X gla domain (EC 3.4.21.6) | protein | 44 | 59% helix, 0% strand | P00743 |
Ligands and binding sites
- CA · Calcium ion · metal · 12 copies · chains A, B, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 284 | 0.70 | 0.85 | 38 | empty |
| 2 | 66 | 0.37 | 0.78 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1945 Ų buried · 27 hydrogen bonds · protein-protein
- B–G · 495 Ų buried · 9 hydrogen bonds · protein-protein
- A–G · 386 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified, 8 disulfide (carboxylation, disulfide).
Compared structures
- 1IOD · Crystal structure of the complex between the coagulation factor X binding protein from… · the same entry in another collection · chain A against A, TM-score 1.00
- P00743 · AlphaFold monomer V2.0 prediction for coagulation factor X (P00743) · a predicted model of the same protein · chain G against A, TM-score 0.88
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P00743
- Elsewhere: RCSB PDB 1IOD · PDBe 1IOD · UniProt P00743
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