MolNFT v1 · #173645 · protein
Crystal structure of mure from E.COLI in complex with Z57715447
7B6K · Udp-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6…: “Crystal structure of mure from E.COLI in complex with Z57715447”. X-ray diffraction, 1 ligand (SZ2), 17 pockets (best druggability 0.70). MolNFT v1 #173645 on GenesisL1: 3D structure…
- PDB
- 7B6K
- Type
- protein
- Length
- 957 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
- SZ2
- Pockets
- 17 · best druggability 0.70
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 | 480 | 35% 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, 24% strand | P22188 |
Ligands and binding sites
- SZ2 · 5-cyclohexyl-3-(pyridin-4-yl)-1,2,4-oxadiazole · ligand · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A, B
- CIT · Citric acid · additive · 2 copies · chains A, B
- IPA · Isopropyl alcohol · additive · chains A
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 | 229 | 0.70 | 0.86 | 38 | DMS, IPA, SZ2 |
| 2 | 492 | 0.67 | 0.79 | 48 | empty |
| 3 | 146 | 0.66 | 0.87 | 25 | SZ2, DMS |
| 4 | 302 | 0.65 | 0.81 | 36 | CIT |
| 5 | 249 | 0.61 | 0.80 | 28 | CIT |
Interfaces
1 interface between chains.
- A–B · 434 Ų buried · 6 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 7B6K · PDBe 7B6K · UniProt P22188
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