MolNFT v1 · #162659 · protein
Crystal structure of egrck-inhibited gla-domainless fixa (K148Q, R150Q variant)
6RFK · Coagulation factor IX: “Crystal structure of egrck-inhibited gla-domainless fixa (K148Q, R150Q variant)”. X-ray diffraction, 2 ligands (CA, 0QE), 1 pocket (best druggability 0.46). MolNFT v1 #162659 on GenesisL1: 3D structure…
- PDB
- 6RFK
- Type
- protein
- Length
- 300 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor IX; Glu-gly-AR7-0QE
- EC
- 3.4.21.22
- UniProt
- P00740
- Ligands
- CA, 0QE
- Pockets
- 1 · best druggability 0.46
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Coagulation factor IX (EC 3.4.21.22) | protein | 62 | 6% helix, 26% strand | P00740 |
| S | Coagulation factor IX (EC 3.4.21.22) | protein | 235 | 13% helix, 37% strand | P00740 |
| I | Glu-gly-AR7-0QE | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · chains S
- 0QE · Chloromethane · ion · chains S, I
- GOL · Glycerol · additive · 10 copies · chains E, S
- B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · chains E, S
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 151 | 0.46 | 0.77 | 21 | empty |
Interfaces
2 interfaces between chains.
- E–S · 808 Ų buried · 6 hydrogen bonds · protein-protein
- S–I · 368 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 modified (disulfide, nonstandard).
Compared structures
- 6RFK · Crystal structure of EGRCK-inhibited Gla-domainless fIXa (K148Q, R150Q variant) · the same entry in another collection · chain E against E, TM-score 1.00
- P00740 · AlphaFold monomer V2.0 prediction for coagulation factor IX (P00740) · a predicted model of the same protein · chain S against A, TM-score 0.98
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 6RFK · PDBe 6RFK · UniProt P00740
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