MolNFT v1 · #27456 · protein
Factor xa complexed with a synthetic inhibitor fx-2212A,(2S)-(3'- amidino-3-biphenylyl)-5-(4-PYRIDYLAMINO)PENTANOIC acid
1XKB · Blood coagulation factor xa: “Factor xa complexed with a synthetic inhibitor fx-2212A,(2S)-(3'…”. X-ray diffraction, 2 ligands (4PP, CA), 8 pockets (best druggability 0.68). MolNFT v1 #27456 on GenesisL1: 3D structure, binding sites…
- PDB
- 1XKB
- Type
- protein
- Length
- 650 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Blood coagulation factor xa
- EC
- 3.4.21.6
- UniProt
- P00742
- Ligands
- 4PP, CA
- Pockets
- 8 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Blood coagulation factor xa (EC 3.4.21.6) | protein | 91 | 4% helix, 24% strand | P00742 |
| C | Blood coagulation factor xa (EC 3.4.21.6) | protein | 235 | 13% helix, 37% strand | P00742 |
| B | Blood coagulation factor xa (EC 3.4.21.6) | protein | 90 | 4% helix, 27% strand | P00742 |
| D | Blood coagulation factor xa (EC 3.4.21.6) | protein | 234 | 13% helix, 36% strand | P00742 |
Ligands and binding sites
- 4PP · (2S)-(3'-amidino-3-biphenyl)-5-(4-pyridylamino)pentanoic acid · ligand · 2 copies · chains C, D
- CA · Calcium ion · metal · 3 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 111 | 0.68 | 0.91 | 28 | empty |
| 2 | 210 | 0.53 | 0.77 | 32 | empty |
| 3 | 169 | 0.48 | 0.76 | 28 | empty |
| 4 | 115 | 0.45 | 0.78 | 32 | 4PP |
| 5 | 108 | 0.42 | 0.77 | 28 | 4PP |
Interfaces
3 interfaces between chains.
- B–D · 912 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 901 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 702 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 disulfide, 2 modified (disulfide, nonstandard).
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 1XKB · PDBe 1XKB · UniProt P00742
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.