MolNFT v1 · #5919 · protein
Human factor xiii, mutant W279F zymogen
1EX0 · Coagulation factor xiii a chain: “Human factor xiii, mutant W279F zymogen”. X-ray diffraction, 2 ligands (CA, PO4), 19 pockets (best druggability 0.87). MolNFT v1 #5919 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1EX0
- Type
- protein
- Length
- 1,421 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor xiii a chain
- EC
- 2.3.2.13
- UniProt
- P00488
- Ligands
- CA, PO4
- Pockets
- 19 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coagulation factor xiii a chain (EC 2.3.2.13) | protein | 705 | 15% helix, 42% strand | P00488 |
| B | Coagulation factor xiii a chain (EC 2.3.2.13) | protein | 716 | 15% helix, 42% strand | P00488 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 3 copies · chains A, B
- PGO · S-1,2-propanediol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1152 | 0.87 | 0.88 | 142 | empty |
| 2 | 959 | 0.77 | 0.80 | 75 | PGO |
| 3 | 252 | 0.68 | 0.84 | 28 | empty |
| 4 | 420 | 0.64 | 0.78 | 34 | empty |
| 5 | 148 | 0.64 | 0.86 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 2584 Ų buried · 39 hydrogen bonds · protein-protein
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 1EX0 · PDBe 1EX0 · UniProt P00488
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