MolNFT v1 · #176528 · protein
Structural basis for ligand binding modes of CTP synthase
7DPT: “Structural basis for ligand binding modes of CTP synthase”. Electron microscopy, 5 ligands (GTP, DON, ADP), 16 pockets (best druggability 0.85). MolNFT v1 #176528 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7DPT
- Type
- protein
- Length
- 2,224 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CTP synthase
- EC
- 6.3.4.2
- UniProt
- Q9VUL1
- Ligands
- GTP, DON, ADP, 5ZL, MG
- Pockets
- 16 · best druggability 0.85
Structure
electron microscopy · 1 distinct chain · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | CTP synthase (EC 6.3.4.2) | protein | 556 | 42% helix, 20% strand | Q9VUL1 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 4 copies · chains A, C, B, D
- DON · 6-diazenyl-5-oxo-L-norleucine · ligand · 4 copies · chains A, B, C, D
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- 5ZL · [[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(2-oxidanyl-4-phosphonooxy-pyrimidin-1-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 12 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 655 | 0.85 | 0.89 | 80 | empty |
| 2 | 1051 | 0.83 | 0.84 | 101 | ADP, MG, 5ZL |
| 3 | 1163 | 0.83 | 0.83 | 91 | MG, ADP, 5ZL |
| 4 | 520 | 0.82 | 0.88 | 65 | empty |
| 5 | 1139 | 0.82 | 0.83 | 89 | MG, ADP, 5ZL |
Interfaces
6 interfaces between chains.
- A–C · 1648 Ų buried · 34 hydrogen bonds · protein-protein
- B–D · 1648 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 1167 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1167 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 447 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
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 Q9VUL1
- Elsewhere: RCSB PDB 7DPT · PDBe 7DPT · UniProt Q9VUL1
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