MolNFT v1 · #114459 · protein
Crystal structure of udp-N-acetylglucosamine 1-carboxyvinyltransferase (udp-N-acetylglucosamine enolpyruvyl transferase, ept) from pseudomonas aeruginosa
5BQ2: “Crystal structure of udp-N-acetylglucosamine 1-carboxyvinyltransferase (udp-N-acetylglucosamine enolpyruvyl…”. X-ray diffraction, 2 ligands (EPU, MG), 19 pockets (best druggability 0.87). MolNFT v1 #114459 on GenesisL1: 3D…
- PDB
- 5BQ2
- Type
- protein
- Length
- 1,700 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-N-acetylglucosamine 1-carboxyvinyltransferase
- EC
- 2.5.1.7
- UniProt
- Q9HVW7
- Ligands
- EPU, MG
- Pockets
- 19 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Udp-N-acetylglucosamine 1-carboxyvinyltransferase (EC 2.5.1.7) | protein | 425 | 34% helix, 26% strand | Q9HVW7 |
Ligands and binding sites
- EPU · Uridine-diphosphate-2(N-acetylglucosaminyl) butyric acid · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 703 | 0.87 | 0.91 | 89 | EPU |
| 2 | 413 | 0.85 | 0.93 | 68 | EPU |
| 3 | 517 | 0.85 | 0.91 | 69 | EPU |
| 4 | 277 | 0.81 | 0.93 | 50 | EPU |
| 5 | 827 | 0.75 | 0.79 | 110 | MG |
Interfaces
6 interfaces between chains.
- A–B · 1296 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1238 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 900 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 859 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 410 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 5BQ2 · Crystal structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9HVW7 · AlphaFold monomer V2.0 prediction for udp-N-acetylglucosamine 1-carboxyvinyltransferase… · 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 Q9HVW7
- Elsewhere: RCSB PDB 5BQ2 · PDBe 5BQ2 · UniProt Q9HVW7
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