Research workbench
Crystal structure of human fxa in complex with methyl (2Z)-3-[(3- chloro-1H-indol-7-YL)AMINO]-2-cyano-3-{[(3S)-2-oxo-1-(2-oxo-2- pyrrolidin-1-YLETHYL)AZEPAN-3-YL]AMINO}ACRYLATE
Analyse Crystal structure of human fxa in complex with methyl (2Z)-3-[(3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ENS
- Type
- protein
- Length
- 643 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Factor X light chain; Activated factor xa heavy chain
- EC
- 3.4.21.6
- UniProt
- P00742
- Ligands
- ENS, CA, NA
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Factor X light chain (EC 3.4.21.6) | protein | 84 | 5% helix, 29% strand | P00742 |
| B, D | Activated factor xa heavy chain (EC 3.4.21.6) | protein | 238 | 14% helix, 37% strand | P00742 |
| C | Factor X light chain (EC 3.4.21.6) | protein | 83 | 5% helix, 27% strand | P00742 |
Ligands and binding sites
- ENS · methyl (2Z)-3-[(3-chloro-1H-indol-7-yl)amino]-2-cyano-3-{[(3S)-2-oxo-1-(2-oxo-2-pyrrolidin-1-ylethyl)azepan-3-yl]amino}acrylate · ligand · 2 copies · chains B, A, D
- CA · Calcium ion · metal · 2 copies · chains B, D
- NA · Sodium ion · metal · 2 copies · chains B, D
- GOL · Glycerol · additive · 7 copies · chains A, B, C, D
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains B, D
- ACT · Acetate ion · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 500 | 0.74 | 0.82 | 45 | ENS |
| 2 | 584 | 0.68 | 0.77 | 52 | GOL |
| 3 | 158 | 0.46 | 0.76 | 28 | ENS |
| 4 | 131 | 0.44 | 0.77 | 25 | GOL |
| 5 | 116 | 0.39 | 0.75 | 29 | GOL |
Interfaces
4 interfaces between chains.
- A–B · 915 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 903 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 724 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 423 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 22 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 3ENS · PDBe 3ENS · UniProt P00742
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