MolNFT v1 · #157316 · protein
Crystal structure of human coagulation factor ixa
6MV4: “Crystal structure of human coagulation factor ixa”. X-ray diffraction, 5 ligands (PBZ, CA, NA), 2 pockets (best druggability 0.47). MolNFT v1 #157316 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6MV4
- Type
- protein
- Length
- 289 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor IX
- EC
- 3.4.21.22
- UniProt
- P00740
- Ligands
- PBZ, CA, NA, SO4, CL
- Pockets
- 2 · best druggability 0.47
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Coagulation factor IX (EC 3.4.21.22) | protein | 235 | 13% helix, 37% strand | P00740 |
| L | Coagulation factor IX (EC 3.4.21.22) | protein | 54 | 7% helix, 26% strand | P00740 |
Ligands and binding sites
- PBZ · P-amino benzamidine · ligand · chains H
- CA · Calcium ion · metal · chains H
- NA · Sodium ion · metal · chains H
- SO4 · Sulfate ion · ion · 6 copies · chains H
- CL · Chloride ion · ion · 3 copies · chains H
- EDO · 1,2-ethanediol · additive · 2 copies · chains H
- FMT · Formic acid · additive · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 117 | 0.47 | 0.79 | 21 | empty |
| 2 | 104 | 0.43 | 0.78 | 29 | PBZ |
Interfaces
1 interface between chains.
- H–L · 837 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
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 P00740
- Elsewhere: RCSB PDB 6MV4 · PDBe 6MV4 · UniProt P00740
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