Research workbench
Fxiiia in complex with the inhibitor ZED2369
Analyse Fxiiia in complex with the inhibitor ZED2369 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MHO
- Type
- protein
- Length
- 1,365 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor xiii a chain; Inhibitor ZED2369
- EC
- 2.3.2.13
- UniProt
- P00488
- Ligands
- TRM, 1TX, CA, SO4, NH2
- Pockets
- 10 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 16% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coagulation factor xiii a chain (EC 2.3.2.13) | protein | 678 | 16% helix, 39% strand | P00488 |
| B | Coagulation factor xiii a chain (EC 2.3.2.13) | protein | 676 | 16% helix, 40% strand | P00488 |
| G | Inhibitor ZED2369 | protein | 5 | 0% helix, 20% strand | — |
| H | Inhibitor ZED2369 | protein | 6 | 0% helix, 17% strand | — |
Ligands and binding sites
- TRM · 1H-benoximidazole-2-carboxylic acid · ligand · 2 copies · chains A, G, B, H
- 1TX · (2S)-2-amino-7-methoxy-7-oxoheptanoic acid · ligand · 2 copies · chains A, G, B, H
- CA · Calcium ion · metal · 6 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- NH2 · Amino group · ion · chains B, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 408 | 0.64 | 0.78 | 56 | empty |
| 2 | 413 | 0.60 | 0.76 | 52 | empty |
| 3 | 262 | 0.57 | 0.78 | 30 | empty |
| 4 | 66 | 0.41 | 0.80 | 15 | TRM, 1TX |
| 5 | 69 | 0.41 | 0.80 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 698 Ų buried · 7 hydrogen bonds · protein-protein
- B–H · 417 Ų buried · 5 hydrogen bonds · protein-protein
- A–G · 327 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (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 P00488
- Elsewhere: RCSB PDB 5MHO · PDBe 5MHO · UniProt P00488
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