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Crystal structure of dihydroorotase pyrc from yersinia pestis in complex with zinc and malate at 2.4 a resolution
Analyse Crystal structure of dihydroorotase pyrc from yersinia pestis in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CTY
- Type
- protein
- Length
- 2,069 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydroorotase
- EC
- 3.5.2.3
- UniProt
- Q8ZFU4
- Ligands
- MLT, ZN
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydroorotase (EC 3.5.2.3) | protein | 345 | 38% helix, 19% strand | Q8ZFU4 |
| B, D | Dihydroorotase (EC 3.5.2.3) | protein | 343 | 38% helix, 18% strand | Q8ZFU4 |
| C | Dihydroorotase (EC 3.5.2.3) | protein | 353 | 37% helix, 18% strand | Q8ZFU4 |
| E | Dihydroorotase (EC 3.5.2.3) | protein | 341 | 39% helix, 19% strand | Q8ZFU4 |
| F | Dihydroorotase (EC 3.5.2.3) | protein | 344 | 38% helix, 19% strand | Q8ZFU4 |
Ligands and binding sites
- MLT · D-malate · ligand · 5 copies · chains A, B, C, D, F
- ZN · Zinc ion · metal · 12 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 218 | 0.73 | 0.88 | 38 | empty |
| 2 | 608 | 0.70 | 0.78 | 43 | empty |
| 3 | 233 | 0.67 | 0.84 | 36 | empty |
| 4 | 591 | 0.63 | 0.75 | 84 | empty |
| 5 | 330 | 0.61 | 0.78 | 38 | empty |
Interfaces
10 interfaces between chains.
- A–E · 1182 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1180 Ų buried · 21 hydrogen bonds · protein-protein
- B–F · 1176 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 958 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 603 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (oxidation, carboxylation).
Compared structures
- 6CTY · Crystal structure of dihydroorotase pyrC from Yersinia pestis in complex with zinc and… · the same entry in another collection · chain F against F, TM-score 1.00
- Q8ZFU4 · AlphaFold monomer V2.0 prediction for dihydroorotase (Q8ZFU4) · a predicted model of the same protein · chain F 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 Q8ZFU4
- Elsewhere: RCSB PDB 6CTY · PDBe 6CTY · UniProt Q8ZFU4
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