MolNFT v1 · #160075 · protein
Crystal structure of human thrombin mutant W215A
6P9U · Prothrombin: “Crystal structure of human thrombin mutant W215A”. X-ray diffraction, 2 ligands (NAG, ZN), 20 pockets (best druggability 0.80). MolNFT v1 #160075 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6P9U
- Type
- protein
- Length
- 1,107 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prothrombin
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- NAG, ZN
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 6 distinct chains · 15% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prothrombin (EC 3.4.21.5) | protein | 30 | 20% helix, 0% strand | P00734 |
| B | Prothrombin (EC 3.4.21.5) | protein | 245 | 14% helix, 31% strand | P00734 |
| C, E, G | Prothrombin (EC 3.4.21.5) | protein | 31 | 29% helix, 0% strand | P00734 |
| D | Prothrombin (EC 3.4.21.5) | protein | 244 | 14% helix, 33% strand | P00734 |
| F | Prothrombin (EC 3.4.21.5) | protein | 247 | 14% helix, 30% strand | P00734 |
| H | Prothrombin (EC 3.4.21.5) | protein | 248 | 13% helix, 33% strand | P00734 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B, D, F, H
- ZN · Zinc ion · metal · 7 copies · chains A, B, C, H, D, E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 975 | 0.80 | 0.81 | 97 | empty |
| 2 | 700 | 0.75 | 0.81 | 72 | empty |
| 3 | 579 | 0.71 | 0.79 | 71 | empty |
| 4 | 304 | 0.60 | 0.78 | 29 | empty |
| 5 | 59 | 0.59 | 0.91 | 15 | empty |
Interfaces
12 interfaces between chains.
- E–F · 1229 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1208 Ų buried · 23 hydrogen bonds · protein-protein
- G–H · 1196 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1196 Ų buried · 20 hydrogen bonds · protein-protein
- C–H · 608 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6P9U · Crystal structure of human thrombin mutant W215A · the same entry in another collection · chain A against A, TM-score 1.00
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 P00734
- Elsewhere: RCSB PDB 6P9U · PDBe 6P9U · UniProt P00734
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