Research workbench
Crystal structure of factor ixa variant K98T in complex with egr- chloromethylketone
Analyse Crystal structure of factor ixa variant K98T in complex with egr… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JB8
- Type
- protein
- Length
- 286 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
- 0GJ, CA
- Pockets
- 2 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Coagulation factor IX (EC 3.4.21.22) | protein | 51 | 8% helix, 27% strand | P00740 |
| S | Coagulation factor IX (EC 3.4.21.22) | protein | 235 | 12% helix, 36% strand | P00740 |
Ligands and binding sites
- 0GJ · L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide · ligand · chains S
- CA · Calcium ion · metal · chains S
- DMS · Dimethyl sulfoxide · additive · chains S
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 | 165 | 0.48 | 0.76 | 20 | empty |
| 2 | 51 | 0.38 | 0.81 | 22 | 0GJ |
Interfaces
1 interface between chains.
- E–S · 759 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 5JB8 · Crystal structure of factor IXa variant K98T in complex with EGR-chloromethylketone · 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 0.97
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 5JB8 · PDBe 5JB8 · UniProt P00740
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