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Crystal structure of mure from E.COLI in complex with Z57299526
Analyse Crystal structure of mure from E.COLI in complex with Z57299526 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7B68
- Type
- protein
- Length
- 969 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
- LVV
- Pockets
- 17 · best druggability 0.66
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 | 492 | 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, 25% strand | P22188 |
Ligands and binding sites
- LVV · 4-[(4-methylphenyl)methyl]-1,4-thiazinane 1,1-dioxide · ligand · 4 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 3 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 448 | 0.66 | 0.78 | 50 | empty |
| 2 | 452 | 0.65 | 0.78 | 33 | empty |
| 3 | 243 | 0.64 | 0.82 | 27 | empty |
| 4 | 86 | 0.62 | 0.89 | 29 | DMS |
| 5 | 477 | 0.60 | 0.75 | 42 | empty |
Interfaces
1 interface between chains.
- A–B · 450 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 7B68 · PDBe 7B68 · UniProt P22188
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