MolNFT v1 · #105539 · protein
Structure of udp-N-acetylglucosamine 1-carboxyvinyltransferase from vibrio cholerae in complex with substrate udp-N-acetylglucosamine and the drug fosfomycin
4R7U: “Structure of udp-N-acetylglucosamine 1-carboxyvinyltransferase from vibrio cholerae in complex with substrate…”. X-ray diffraction, 3 ligands (FFQ, UD1, NA), 19 pockets (best druggability 0.87). MolNFT v1 #105539 on GenesisL1: 3D…
- PDB
- 4R7U
- Type
- protein
- Length
- 1,673 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
- Q9KP62
- Ligands
- FFQ, UD1, NA
- Pockets
- 19 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Udp-N-acetylglucosamine 1-carboxyvinyltransferase (EC 2.5.1.7) | protein | 418 | 34% helix, 27% strand | Q9KP62 |
| C | Udp-N-acetylglucosamine 1-carboxyvinyltransferase (EC 2.5.1.7) | protein | 419 | 34% helix, 27% strand | Q9KP62 |
Ligands and binding sites
- FFQ · [(1R)-1-hydroxypropyl]phosphonic acid · ligand · 4 copies · chains A, B, C, D
- UD1 · Uridine-diphosphate-N-acetylglucosamine · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 5 copies · chains A, B, C, D
- PG4 · Tetraethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 789 | 0.87 | 0.90 | 108 | UD1, FFQ |
| 2 | 661 | 0.86 | 0.90 | 75 | UD1, FFQ |
| 3 | 675 | 0.86 | 0.90 | 77 | FFQ, UD1 |
| 4 | 467 | 0.83 | 0.90 | 51 | UD1, FFQ |
| 5 | 127 | 0.69 | 0.90 | 33 | NA |
Interfaces
6 interfaces between chains.
- C–D · 1196 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1131 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 806 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 797 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 259 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4R7U · Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Vibrio cholerae in… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9KP62 · AlphaFold monomer V2.0 prediction for udp-N-acetylglucosamine 1-carboxyvinyltransferase… · a predicted model of the same protein · chain C 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 Q9KP62
- Elsewhere: RCSB PDB 4R7U · PDBe 4R7U · UniProt Q9KP62
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