Research workbench
Fxiiia in complex with the inhibitor ZED2360
Analyse Fxiiia in complex with the inhibitor ZED2360 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MHN
- Type
- protein
- Length
- 1,385 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor xiii a chain; Inhibitor ZED2360
- EC
- 2.3.2.13
- UniProt
- P00488
- Ligands
- 7NF, 1TX, CA, SO4
- Pockets
- 10 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coagulation factor xiii a chain (EC 2.3.2.13) | protein | 688 | 16% helix, 41% strand | P00488 |
| B | Coagulation factor xiii a chain (EC 2.3.2.13) | protein | 685 | 17% helix, 41% strand | P00488 |
| H, I | Inhibitor ZED2360 | protein | 6 | 0% helix, 33% strand | — |
Ligands and binding sites
- 7NF · 2-ethoxycarbonyl-1,3-thiazole-4-carboxylic acid · ligand · 2 copies · chains A, H, B, I
- 1TX · (2S)-2-amino-7-methoxy-7-oxoheptanoic acid · ligand · 2 copies · chains A, H, B, I
- CA · Calcium ion · metal · 6 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
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 | 344 | 0.61 | 0.78 | 43 | GOL |
| 2 | 299 | 0.60 | 0.78 | 39 | GOL |
| 3 | 362 | 0.58 | 0.76 | 41 | empty |
| 4 | 91 | 0.44 | 0.79 | 23 | 7NF, 1TX |
| 5 | 67 | 0.42 | 0.81 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 719 Ų buried · 9 hydrogen bonds · protein-protein
- A–H · 453 Ų buried · 5 hydrogen bonds · protein-protein
- B–I · 406 Ų buried · 4 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 5MHN · PDBe 5MHN · UniProt P00488
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