MolNFT v1 · #135622 · protein
1.05 ångström resolution crystal structure of udp-N-acetylglucosamine 1-carboxyvinyltransferase from acinetobacter baumannii in covalently bound complex with (2R)-2-(PHOSPHONOOXY)PROPANOIC acid.
5U4H: “1.05 ångström resolution crystal structure of udp-N-acetylglucosamine 1-carboxyvinyltransferase from…”. X-ray diffraction, 2 ligands (0V5, NA), 4 pockets (best druggability 0.87). MolNFT v1 #135622 on GenesisL1: 3D structure…
- PDB
- 5U4H
- Type
- protein
- Length
- 840 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-N-acetylglucosamine 1-carboxyvinyltransferase
- EC
- 2.5.1.7
- UniProt
- A0A0R0VXX6
- Ligands
- 0V5, NA
- Pockets
- 4 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Udp-N-acetylglucosamine 1-carboxyvinyltransferase (EC 2.5.1.7) | protein | 420 | 35% helix, 27% strand | A0A0R0VXX6 |
Ligands and binding sites
- 0V5 · (2R)-2-(phosphonooxy)propanoic acid · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 9 copies · chains A, B
- FMT · Formic acid · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1077 | 0.87 | 0.88 | 117 | NA, FMT, 0V5 |
| 2 | 482 | 0.82 | 0.89 | 50 | NA, FMT, 0V5 |
| 3 | 84 | 0.36 | 0.76 | 17 | empty |
| 4 | 58 | 0.31 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1154 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5U4H · 1.05 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosamine… · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A0R0VXX6
- Elsewhere: RCSB PDB 5U4H · PDBe 5U4H · UniProt A0A0R0VXX6
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