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Crystal structure of mure from E.COLI in complex with Z1198948504
Analyse Crystal structure of mure from E.COLI in complex with Z1198948504 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7B6M
- 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
- SZN
- Pockets
- 17 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 36% 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 | 36% helix, 25% strand | P22188 |
Ligands and binding sites
- SZN · N-[2-(2,5-Dioxopyrrolidin-1-yl)ethyl]-3-methylbenzamide · ligand · chains B
- EDO · 1,2-ethanediol · 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 204 | 0.82 | 0.95 | 32 | empty |
| 2 | 234 | 0.81 | 0.94 | 31 | SZN |
| 3 | 918 | 0.72 | 0.77 | 65 | empty |
| 4 | 342 | 0.68 | 0.82 | 37 | empty |
| 5 | 279 | 0.61 | 0.80 | 29 | EDO |
Interfaces
1 interface between chains.
- A–B · 420 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
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 7B6M · PDBe 7B6M · UniProt P22188
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