MolNFT v1 · #112180 · protein
Crystal structure of the M. tuberculosis CTP synthase pyrg (apo form)
4ZDI: “Crystal structure of the M. tuberculosis CTP synthase pyrg (apo form)”. X-ray diffraction, 1 ligand (CA), 20 pockets (best druggability 0.80). MolNFT v1 #112180 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4ZDI
- Type
- protein
- Length
- 4,237 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CTP synthase
- EC
- 6.3.4.2
- UniProt
- P9WHK7
- Ligands
- CA
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 8 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CTP synthase (EC 6.3.4.2) | protein | 531 | 39% helix, 23% strand | P9WHK7 |
| B | CTP synthase (EC 6.3.4.2) | protein | 534 | 40% helix, 23% strand | P9WHK7 |
| C | CTP synthase (EC 6.3.4.2) | protein | 533 | 40% helix, 23% strand | P9WHK7 |
| D | CTP synthase (EC 6.3.4.2) | protein | 531 | 40% helix, 24% strand | P9WHK7 |
| E | CTP synthase (EC 6.3.4.2) | protein | 530 | 40% helix, 23% strand | P9WHK7 |
| F | CTP synthase (EC 6.3.4.2) | protein | 526 | 40% helix, 23% strand | P9WHK7 |
| G | CTP synthase (EC 6.3.4.2) | protein | 527 | 39% helix, 22% strand | P9WHK7 |
| H | CTP synthase (EC 6.3.4.2) | protein | 525 | 39% helix, 24% strand | P9WHK7 |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 586 | 0.80 | 0.86 | 53 | empty |
| 2 | 179 | 0.79 | 0.94 | 42 | empty |
| 3 | 181 | 0.75 | 0.91 | 32 | empty |
| 4 | 153 | 0.75 | 0.92 | 29 | empty |
| 5 | 154 | 0.74 | 0.92 | 32 | empty |
Interfaces
10 interfaces between chains.
- F–G · 1441 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1439 Ų buried · 20 hydrogen bonds · protein-protein
- E–H · 1274 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 639 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 628 Ų buried · 8 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 P9WHK7
- Elsewhere: RCSB PDB 4ZDI · PDBe 4ZDI · UniProt P9WHK7
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