MolNFT v1 · #106812 · protein
Crystal structure of dihydropyrimidinase from brucella suis
4TQT · D-hydantoinase: “Crystal structure of dihydropyrimidinase from brucella suis”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.85). MolNFT v1 #106812 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4TQT
- Type
- protein
- Length
- 2,869 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-hydantoinase
- EC
- 3.5.2.2
- UniProt
- Q8G2P0
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E | D-hydantoinase (EC 3.5.2.2) | protein | 477 | 36% helix, 22% strand | Q8G2P0 |
| C | D-hydantoinase (EC 3.5.2.2) | protein | 476 | 37% helix, 22% strand | Q8G2P0 |
| D, F | D-hydantoinase (EC 3.5.2.2) | protein | 481 | 36% helix, 22% strand | Q8G2P0 |
Ligands and binding sites
- ZN · Zinc ion · metal · 12 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 24 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1034 | 0.85 | 0.86 | 94 | EDO |
| 2 | 1161 | 0.85 | 0.86 | 117 | EDO |
| 3 | 1079 | 0.84 | 0.85 | 101 | EDO |
| 4 | 633 | 0.79 | 0.84 | 74 | empty |
| 5 | 607 | 0.76 | 0.82 | 58 | empty |
Interfaces
6 interfaces between chains.
- B–D · 2023 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 1934 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 1366 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1361 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1351 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (carboxylation).
Compared structures
- 4TQT · Crystal structure of Dihydropyrimidinase from Brucella suis · 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 Q8G2P0
- Elsewhere: RCSB PDB 4TQT · PDBe 4TQT · UniProt Q8G2P0
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