Research workbench
X-ray crystal structure of the "closed" conformation of CTP-inhibited E. COLI cytidine triphosphate (CTP) synthetase
Analyse X-ray crystal structure of the "closed" conformation of CTP-inhibited E. COLI… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TKV
- Type
- protein
- Length
- 1,067 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CTP synthase
- EC
- 6.3.4.2
- UniProt
- P0A7E5
- Ligands
- GLN, CTP, MG, SO4
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CTP synthase (EC 6.3.4.2) | protein | 532 | 39% helix, 22% strand | P0A7E5 |
| B | CTP synthase (EC 6.3.4.2) | protein | 535 | 41% helix, 22% strand | P0A7E5 |
Ligands and binding sites
- GLN · Glutamine · ligand · 2 copies · chains A, B
- CTP · Cytidine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 790 | 0.74 | 0.79 | 76 | MG, CTP, SO4, MPD |
| 2 | 116 | 0.72 | 0.93 | 27 | GLN |
| 3 | 656 | 0.69 | 0.77 | 57 | SO4, MPD, CTP, MG |
| 4 | 112 | 0.68 | 0.91 | 27 | GLN |
| 5 | 133 | 0.60 | 0.85 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 776 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5TKV · X-ray crystal structure of the closed" conformation of CTP-inhibited E. COLI cytidine… · the same entry in another collection · chain B against B, TM-score 1.00
- P0A7E5 · AlphaFold monomer V2.0 prediction for CTP synthase (P0A7E5) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P0A7E5
- Elsewhere: RCSB PDB 5TKV · PDBe 5TKV · UniProt P0A7E5
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