MolNFT v1 · #28344 · protein
Mura inhibited by a derivative of 5-sulfonoxy-anthranilic acid
1YBG · Udp-N-acetylglucosamine 1-carboxyvinyltransferase: “Mura inhibited by a derivative of 5-sulfonoxy-anthranilic acid”. X-ray diffraction, 1 ligand (TAV), 14 pockets (best druggability 0.77). MolNFT v1 #28344 on GenesisL1: 3D…
- PDB
- 1YBG
- 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
- P33038
- Ligands
- TAV
- Pockets
- 14 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 28% 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 | 33% helix, 28% strand | P33038 |
Ligands and binding sites
- TAV · N-methyl-N-{2-[(2-naphthylsulfonyl)amino]-5-[(2-naphthylsulfonyl)oxy]benzoyl}-L-aspartic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 808 | 0.77 | 0.81 | 113 | TAV |
| 2 | 688 | 0.76 | 0.81 | 87 | TAV |
| 3 | 436 | 0.75 | 0.84 | 71 | TAV |
| 4 | 486 | 0.74 | 0.83 | 83 | TAV |
| 5 | 282 | 0.71 | 0.85 | 46 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1148 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1133 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 799 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 695 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 588 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 1YBG · MurA inhibited by a derivative of 5-sulfonoxy-anthranilic acid · the same entry in another collection · chain A against A, TM-score 1.00
- P33038 · AlphaFold monomer V2.0 prediction for udp-N-acetylglucosamine 1-carboxyvinyltransferase… · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P33038
- Elsewhere: RCSB PDB 1YBG · PDBe 1YBG · UniProt P33038
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