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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
- 7B61
- Type
- protein
- Length
- 959 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
- SYQ, T3Z
- Pockets
- 15 · best druggability 0.79
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 | 480 | 36% helix, 25% strand | P22188 |
| B | Udp-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6- diaminopimelate ligase (EC 6.3.2.13) | protein | 479 | 36% helix, 25% strand | P22188 |
Ligands and binding sites
- SYQ · (S)-N-(1-cyclopropylethyl)-6-methylpicolinamide · ligand · 2 copies · chains A, B
- T3Z · (R)-N-(1-cyclopropylethyl)-6-methylpicolinamide · ligand · 2 copies · chains A, B
- IPA · Isopropyl alcohol · additive · 4 copies · chains A, B
- CIT · Citric acid · additive · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 197 | 0.79 | 0.93 | 28 | T3Z |
| 2 | 197 | 0.78 | 0.92 | 30 | T3Z |
| 3 | 904 | 0.72 | 0.76 | 60 | IPA |
| 4 | 348 | 0.67 | 0.81 | 40 | CIT |
| 5 | 362 | 0.67 | 0.81 | 36 | CIT |
Interfaces
1 interface between chains.
- A–B · 408 Ų buried · 7 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 7B61 · PDBe 7B61 · UniProt P22188
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