Research workbench
Anti-fx Fab of MIM8 in complex with human fxa
Analyse Anti-fx Fab of MIM8 in complex with human fxa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AHU
- Type
- protein
- Length
- 1,447 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-fx Fab of MIM8 light chain; Anti-fx Fab of MIM8 heavy chain; Coagulation factor X
- EC
- 3.4.21.6
- UniProt
- P00742
- Ligands
- 0GJ, CA
- Pockets
- 16 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 9% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, A | Anti-fx Fab of MIM8 light chain | protein | 216 | 6% helix, 52% strand | — |
| H, B | Anti-fx Fab of MIM8 heavy chain | protein | 222 | 8% helix, 50% strand | — |
| C, E | Coagulation factor X (EC 3.4.21.6) | protein | 234 | 13% helix, 37% strand | P00742 |
| D | Coagulation factor X (EC 3.4.21.6) | protein | 52 | 8% helix, 31% strand | P00742 |
| F | Coagulation factor X (EC 3.4.21.6) | protein | 51 | 8% helix, 31% strand | P00742 |
Ligands and binding sites
- 0GJ · L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide · ligand · 2 copies · chains C, E
- CA · Calcium ion · metal · 2 copies · chains C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 784 | 0.83 | 0.86 | 97 | empty |
| 2 | 537 | 0.76 | 0.84 | 75 | empty |
| 3 | 62 | 0.55 | 0.89 | 20 | empty |
| 4 | 358 | 0.55 | 0.74 | 46 | empty |
| 5 | 293 | 0.53 | 0.75 | 43 | empty |
Interfaces
12 interfaces between chains.
- A–B · 1841 Ų buried · 11 hydrogen bonds · protein-protein
- L–H · 1773 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 889 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 860 Ų buried · 9 hydrogen bonds · protein-protein
- H–C · 528 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 disulfide, 4 covalent (disulfide, covalent ligand).
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 7AHU · PDBe 7AHU · UniProt P00742
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