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Structure of mura (udp-N-acetylglucosamine enolpyruvyl transferase), from vibrio fischeri in complex with substrate udp-N- acetylglucosamine and the drug fosfomycin.
Analyse Structure of mura (udp-N-acetylglucosamine enolpyruvyl transferase), from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VCY
- Type
- protein
- Length
- 1,676 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
- B5F9P4
- Ligands
- FFQ, UD1, PO4
- Pockets
- 17 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 36% 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 | 419 | 36% helix, 26% strand | B5F9P4 |
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
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 120 | 0.75 | 0.94 | 29 | UD1, PO4, GOL |
| 2 | 106 | 0.72 | 0.94 | 26 | UD1, PO4 |
| 3 | 85 | 0.70 | 0.94 | 28 | UD1, PO4, GOL |
| 4 | 60 | 0.67 | 0.95 | 18 | UD1, GOL |
| 5 | 71 | 0.64 | 0.92 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1298 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1282 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 893 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 888 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 354 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 3VCY · Structure of MurA (UDP-N-acetylglucosamine enolpyruvyl transferase), from Vibrio fischeri… · the same entry in another collection · chain A against A, TM-score 1.00
- B5F9P4 · 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 B5F9P4
- Elsewhere: RCSB PDB 3VCY · PDBe 3VCY · UniProt B5F9P4
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