Research workbench
Human coagulation factor xa in complex with M54471
Analyse Human coagulation factor xa in complex with M54471 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IQM
- 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
- XMK, CA
- Pockets
- 3 · best druggability 0.42
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coagulation factor xa (EC 3.4.21.6) | protein | 235 | 13% helix, 36% strand | P00742 |
| L | Coagulation factor xa (EC 3.4.21.6) | protein | 51 | 14% helix, 25% strand | P00742 |
Ligands and binding sites
- XMK · 1-[[(1E)-2-(4-chlorophenyl)ethenyl]sulfonyl]-4-[[1-(4-pyridinyl)-4-piperidinyl]methyl]piperazine · 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 | 100 | 0.42 | 0.78 | 24 | XMK |
| 2 | 57 | 0.30 | 0.74 | 11 | empty |
| 3 | 61 | 0.29 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–L · 909 Ų buried · 10 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 1IQM · PDBe 1IQM · UniProt P00742
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