Research workbench
Crystal structure of factor ixa variant V16I K98T Y177T I212V in complex with ppack
Analyse Crystal structure of factor ixa variant V16I K98T Y177T I212V in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JBA
- 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
- 0G6, 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
- 0G6 · D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide · 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 | 120 | 0.48 | 0.79 | 20 | empty |
| 2 | 136 | 0.43 | 0.76 | 31 | 0G6 |
Interfaces
1 interface between chains.
- E–S · 752 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 5JBA · Crystal structure of factor IXa variant V16I K98T Y177T I212V in complex with PPACK · 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 5JBA · PDBe 5JBA · UniProt P00740
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