Research workbench
Crystal structure of mure from E.COLI in complex with minifrag succinimide
Analyse Crystal structure of mure from E.COLI in complex with minifrag succinimide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7B6J
- Type
- protein
- Length
- 964 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
- SZB
- Pockets
- 17 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 25% 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 | 487 | 36% helix, 25% strand | P22188 |
| B | Udp-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6- diaminopimelate ligase (EC 6.3.2.13) | protein | 477 | 35% helix, 25% strand | P22188 |
Ligands and binding sites
- SZB · succinimide · ligand · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- IPA · Isopropyl alcohol · additive · 2 copies · chains A, 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 | 212 | 0.80 | 0.94 | 35 | EDO, SZB, IPA |
| 2 | 994 | 0.75 | 0.78 | 80 | empty |
| 3 | 403 | 0.65 | 0.79 | 41 | empty |
| 4 | 193 | 0.64 | 0.84 | 36 | SZB, IPA |
| 5 | 400 | 0.64 | 0.78 | 41 | empty |
Interfaces
1 interface between chains.
- A–B · 404 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7B6J · Crystal structure of MurE from E.coli in complex with minifrag succinimide · 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 0.79
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 7B6J · PDBe 7B6J · UniProt P22188
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.