Research workbench
Human coagulation factor xa in complex with M55125
Analyse Human coagulation factor xa in complex with M55125 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IQI
- Type
- protein
- Length
- 286 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor xa
- EC
- 3.4.21.6
- UniProt
- P00742
- Ligands
- XMG, CA
- Pockets
- 3 · best druggability 0.40
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coagulation factor xa (EC 3.4.21.6) | protein | 235 | 11% helix, 34% strand | P00742 |
| L | Coagulation factor xa (EC 3.4.21.6) | protein | 51 | 14% helix, 24% strand | P00742 |
Ligands and binding sites
- XMG · 4-[(6-chloro-2-naphthalenyl)sulfonyl]-1-[[1-(4-pyridinyl)-4-piperidinyl] methyl]-2-piperazinecarboxylic acid · ligand · chains A
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 90 | 0.40 | 0.77 | 23 | XMG |
| 2 | 87 | 0.32 | 0.73 | 22 | empty |
| 3 | 59 | 0.32 | 0.76 | 12 | empty |
Interfaces
1 interface between chains.
- A–L · 877 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 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 P00742
- Elsewhere: RCSB PDB 1IQI · PDBe 1IQI · UniProt P00742
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