Research workbench
Crystal structure of the M. tuberculosis CTP synthase pyrg in complex with UTP, AMP-pcp and oxonorleucine
Analyse Crystal structure of the M. tuberculosis CTP synthase pyrg in complex with UTP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZDK
- Type
- protein
- Length
- 1,068 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CTP synthase
- EC
- 6.3.4.2
- UniProt
- P9WHK7
- Ligands
- ONL, ACP, UTP, MG
- Pockets
- 14 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | CTP synthase (EC 6.3.4.2) | protein | 534 | 42% helix, 23% strand | P9WHK7 |
Ligands and binding sites
- ONL · 5-oxo-L-norleucine · ligand · 2 copies · chains A, B
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 2 copies · chains A, B
- UTP · Uridine 5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 170 | 0.76 | 0.92 | 27 | ONL |
| 2 | 150 | 0.75 | 0.92 | 27 | ONL |
| 3 | 828 | 0.69 | 0.75 | 87 | empty |
| 4 | 51 | 0.68 | 0.97 | 25 | empty |
| 5 | 51 | 0.64 | 0.94 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 386 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4ZDK · Crystal structure of the M. tuberculosis CTP synthase PyrG in complex with UTP, AMP-PCP… · the same entry in another collection · chain A against A, TM-score 1.00
- P9WHK7 · AlphaFold monomer V2.0 prediction for CTP synthase (P9WHK7) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P9WHK7
- Elsewhere: RCSB PDB 4ZDK · PDBe 4ZDK · UniProt P9WHK7
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