Research workbench
Crystal structure of blood coagulation factor xa in complex with ecotin M84R
Analyse Crystal structure of blood coagulation factor xa in complex with ecotin M84R in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1P0S
- Type
- protein
- Length
- 473 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor X precursor; Ecotin precursor
- EC
- 3.4.21.6
- UniProt
- P00742, P23827
- Ligands
- MG, NA
- Pockets
- 5 · best druggability 0.48
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Coagulation factor X precursor (EC 3.4.21.6) | protein | 99 | 31% helix, 14% strand | P00742 |
| H | Coagulation factor X precursor (EC 3.4.21.6) | protein | 235 | 13% helix, 37% strand | P00742 |
| E | Ecotin precursor | protein | 139 | 4% helix, 47% strand | P23827 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 222 | 0.48 | 0.74 | 32 | empty |
| 2 | 186 | 0.48 | 0.76 | 31 | empty |
| 3 | 127 | 0.43 | 0.76 | 28 | empty |
| 4 | 54 | 0.38 | 0.80 | 15 | empty |
| 5 | 73 | 0.33 | 0.75 | 18 | empty |
Interfaces
2 interfaces between chains.
- H–E · 1022 Ų buried · 29 hydrogen bonds · protein-protein
- L–H · 843 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 modified, 10 disulfide (carboxylation, disulfide).
Compared structures
- 1P0S · Crystal Structure of Blood Coagulation Factor Xa in Complex with Ecotin M84R · the same entry in another collection · chain L against L, TM-score 1.00
- P00742 · AlphaFold monomer V2.0 prediction for coagulation factor X (P00742) · a predicted model of the same protein · chain H against A, TM-score 0.98
- P23827 · AlphaFold monomer V2.0 prediction for ecotin (P23827) · a predicted model of the same protein · chain E 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 P00742
- Every structure of UniProt P23827
- Elsewhere: RCSB PDB 1P0S · PDBe 1P0S · UniProt P00742 · UniProt P23827
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