Research workbench
Structure of mure the udp-N-acetylmuramyl tripeptide synthetase from E. COLI
Analyse Structure of mure the udp-N-acetylmuramyl tripeptide synthetase from E. COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1E8C
- Type
- protein
- Length
- 992 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase
- EC
- 6.3.2.13
- UniProt
- P22188
- Ligands
- UAG, API, CL
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase (EC 6.3.2.13) | protein | 495 | 35% helix, 23% strand | P22188 |
| B | Udp-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase (EC 6.3.2.13) | protein | 497 | 34% helix, 23% strand | P22188 |
Ligands and binding sites
- UAG · Uridine-5'-diphosphate-N-acetylmuramoyl-L-alanine-D-glutamate · ligand · 2 copies · chains A, B
- API · 2,6-diaminopimelic acid · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 427 | 0.76 | 0.86 | 56 | API |
| 2 | 641 | 0.76 | 0.82 | 81 | API |
| 3 | 921 | 0.74 | 0.78 | 92 | UAG |
| 4 | 198 | 0.59 | 0.81 | 27 | empty |
| 5 | 323 | 0.52 | 0.74 | 39 | UAG |
Interfaces
1 interface between chains.
- A–B · 696 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 modified (engineered, carboxylation).
Compared structures
- 1E8C · Structure of MurE the UDP-N-acetylmuramyl tripeptide synthetase from E. coli · the same entry in another collection · chain A against A, TM-score 1.00
- P22188 · AlphaFold monomer V2.0 prediction for udp-N-acetylmuramoyl-L-alanyl… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P22188
- Elsewhere: RCSB PDB 1E8C · PDBe 1E8C · UniProt P22188
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