MolNFT v1 · #126927 · protein
Fxiiia in complex with the inhibitor ZED1630
5MHM · Coagulation factor xiii a chain: “Fxiiia in complex with the inhibitor ZED1630”. X-ray diffraction, 6 ligands (7NW, 1TX, CA), 10 pockets (best druggability 0.63). MolNFT v1 #126927 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5MHM
- Type
- protein
- Length
- 1,377 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor xiii a chain; Inhibitor ZED1630
- EC
- 2.3.2.13
- UniProt
- P00488
- Ligands
- 7NW, 1TX, CA, SO4, NH2, CL
- Pockets
- 10 · best druggability 0.63
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 | 684 | 17% helix, 41% strand | P00488 |
| B | Coagulation factor xiii a chain (EC 2.3.2.13) | protein | 683 | 16% helix, 42% strand | P00488 |
| H, O | Inhibitor ZED1630 | protein | 5 | 0% helix, 20% strand | — |
Ligands and binding sites
- 7NW · 2-methyl-1,3-thiazole-4-carboxylic acid · ligand · 2 copies · chains A, H, B, O
- 1TX · (2S)-2-amino-7-methoxy-7-oxoheptanoic acid · ligand · 2 copies · chains A, H, B, O
- CA · Calcium ion · metal · 6 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- NH2 · Amino group · ion · 2 copies · chains A, H, O
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 6 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 | 400 | 0.63 | 0.78 | 54 | GOL |
| 2 | 323 | 0.61 | 0.78 | 37 | GOL |
| 3 | 404 | 0.60 | 0.76 | 45 | GOL |
| 4 | 72 | 0.41 | 0.79 | 21 | 7NW, 1TX |
| 5 | 64 | 0.41 | 0.81 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 734 Ų buried · 8 hydrogen bonds · protein-protein
- B–O · 392 Ų buried · 5 hydrogen bonds · protein-protein
- A–H · 387 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 2 modified (covalent ligand, nonstandard).
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 5MHM · PDBe 5MHM · UniProt P00488
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