MolNFT v1 · #90044 · protein
E. cloacae C115D mura in complex with udp-glucose
4E7E · Udp-N-acetylglucosamine 1-carboxyvinyltransferase: “E. cloacae C115D mura in complex with udp-glucose”. X-ray diffraction, 1 ligand (UPG), 14 pockets (best druggability 0.82). MolNFT v1 #90044 on GenesisL1: 3D structure, binding…
- PDB
- 4E7E
- 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
- UPG
- Pockets
- 14 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 27% 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 | 32% helix, 27% strand | P33038 |
Ligands and binding sites
- UPG · Uridine-5'-diphosphate-glucose · ligand · 2 copies · chains A, D
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 2 copies · chains A, 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 973 | 0.82 | 0.83 | 97 | empty |
| 2 | 1156 | 0.79 | 0.81 | 136 | EDO, ACT, UPG |
| 3 | 498 | 0.77 | 0.85 | 54 | empty |
| 4 | 562 | 0.77 | 0.84 | 57 | empty |
| 5 | 356 | 0.68 | 0.81 | 46 | empty |
Interfaces
6 interfaces between chains.
- A–D · 811 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 787 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 755 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 729 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 668 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 4E7E · E. cloacae C115D MurA in complex with UDP-glucose · the same entry in another collection · chain D against D, 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 4E7E · PDBe 4E7E · UniProt P33038
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