Research workbench
Factor xa - cation inhibitor complex
Analyse Factor xa - cation inhibitor complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y5G
- Type
- protein
- Length
- 287 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Activated factor xa heavy chain; Factor X light chain
- EC
- 3.4.21.6
- UniProt
- P00742
- Ligands
- FJD, NA
- Pockets
- 3 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Activated factor xa heavy chain (EC 3.4.21.6) | protein | 233 | 13% helix, 36% strand | P00742 |
| L | Factor X light chain (EC 3.4.21.6) | protein | 54 | 7% helix, 26% strand | P00742 |
Ligands and binding sites
- FJD · 3-[(3as,4r,5s,8as,8br)-4-[5-(5-chlorothiophen-2-yl)-1,3-oxazol-2-yl]-1,3-dioxo-4,6,7,8,8A,8B-hexahydro-3AH-pyrrolo[3,4-a]pyrrolizin-2-yl]propyl-trimethyl-azanium · ligand · chains A
- NA · Sodium ion · metal · 2 copies · 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 | 172 | 0.49 | 0.77 | 30 | FJD |
| 2 | 109 | 0.42 | 0.77 | 24 | empty |
| 3 | 50 | 0.30 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–L · 931 Ų buried · 11 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 2Y5G · PDBe 2Y5G · UniProt P00742
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