Research workbench
Crystal structure of mure from E.COLI in complex with Z1269139261
Analyse Crystal structure of mure from E.COLI in complex with Z1269139261 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7B60
- 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
- O3D
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 35% 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 | 487 | 35% helix, 24% 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
- O3D · 4-[(furan-2-yl)methyl]-1lambda~6~,4-thiazinane-1,1-dione · ligand · 3 copies · chains A, B
- DMS · Dimethyl sulfoxide · 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
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 861 | 0.71 | 0.76 | 60 | empty |
| 2 | 241 | 0.62 | 0.81 | 26 | empty |
| 3 | 291 | 0.62 | 0.80 | 29 | empty |
| 4 | 440 | 0.59 | 0.75 | 39 | IPA |
| 5 | 108 | 0.52 | 0.82 | 17 | O3D |
Interfaces
1 interface between chains.
- A–B · 411 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 7B60 · PDBe 7B60 · UniProt P22188
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