MolNFT v1 · #10651 · protein
Crystal structure of coagulation factors IX/X-binding protein (IX/X- bp) from venom of habu snake with a heterodimer of C-type lectin domains
1IXX: “Crystal structure of coagulation factors IX/X-binding protein (IX/X- bp) from venom of habu snake with a…”. X-ray diffraction, 1 ligand (CA), 6 pockets (best druggability 0.79). MolNFT v1 #10651 on GenesisL1: 3D structure, binding…
- PDB
- 1IXX
- Type
- protein
- Length
- 756 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factors IX/X-binding protein
- UniProt
- P23806, P23807
- Ligands
- CA
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Coagulation factors IX/X-binding protein | protein | 129 | 24% helix, 29% strand | P23806 |
| B, D, F | Coagulation factors IX/X-binding protein | protein | 123 | 20% helix, 36% strand | P23807 |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1106 | 0.79 | 0.81 | 103 | empty |
| 2 | 571 | 0.73 | 0.81 | 56 | empty |
| 3 | 178 | 0.54 | 0.80 | 22 | empty |
| 4 | 98 | 0.51 | 0.83 | 18 | empty |
| 5 | 158 | 0.45 | 0.76 | 30 | empty |
Interfaces
12 interfaces between chains.
- A–B · 1928 Ų buried · 32 hydrogen bonds · protein-protein
- E–F · 1915 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1907 Ų buried · 30 hydrogen bonds · protein-protein
- B–F · 399 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 389 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 disulfide (disulfide).
Compared structures
- 1IXX · Crystal structure of coagulation factors IX/X-binding protein (IX/X-bp) from venom of… · the same entry in another collection · chain F against F, TM-score 1.00
- P23807 · AlphaFold monomer V2.0 prediction for snaclec coagulation factor IX/FACTOR X-binding… · a predicted model of the same protein · chain B against A, TM-score 0.92
- P23806 · AlphaFold monomer V2.0 prediction for snaclec coagulation factor IX/FACTOR X-binding… · a predicted model of the same protein · chain A against A, TM-score 0.79
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 P23806
- Every structure of UniProt P23807
- Elsewhere: RCSB PDB 1IXX · PDBe 1IXX · UniProt P23806 · UniProt P23807
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