MolNFT v1 · #17675 · protein
Crystal structure of blood coagulation factor xa in complex with ecotin M84R
1P0S · Coagulation factor X precursor: “Crystal structure of blood coagulation factor xa in complex with ecotin M84R”. X-ray diffraction, 2 ligands (MG, NA), 5 pockets (best druggability 0.48). MolNFT v1 #17675 on GenesisL1: 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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