Research workbench
Crystal structure of E.COLI mure - C269S C340S C450S in complex with ELLMAN'S reagent
Analyse Crystal structure of E.COLI mure - C269S C340S C450S in complex with ELLMAN'S… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7B6P
- Type
- protein
- Length
- 957 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6- diaminopimelate ligase
- EC
- 6.3.2.13
- UniProt
- P22188
- Ligands
- 9JT
- Pockets
- 17 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6- diaminopimelate ligase (EC 6.3.2.13) | protein | 480 | 36% helix, 24% strand | P22188 |
| B | Udp-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6- diaminopimelate ligase (EC 6.3.2.13) | protein | 477 | 36% helix, 24% strand | P22188 |
Ligands and binding sites
- 9JT · ~{N}-phenyl-2-selanyl-benzamide · ligand · 2 copies · chains A, B
- IPA · Isopropyl alcohol · additive · 3 copies · chains A, B
- CIT · Citric acid · additive · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 233 | 0.81 | 0.94 | 31 | 9JT, IPA |
| 2 | 231 | 0.81 | 0.93 | 32 | 9JT, IPA |
| 3 | 824 | 0.71 | 0.77 | 71 | empty |
| 4 | 338 | 0.66 | 0.81 | 38 | CIT |
| 5 | 324 | 0.66 | 0.81 | 36 | CIT |
Interfaces
1 interface between chains.
- A–B · 402 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7B6P · Crystal structure of E.coli MurE - C269S C340S C450S in complex with Ellman's reagent · 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 B against A, TM-score 0.80
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 7B6P · PDBe 7B6P · UniProt P22188
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.