MolNFT v1 · #173651 · protein
Crystal structure of mure from E.COLI in complex with Z57299526
7B6Q · Udp-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6…: “Crystal structure of mure from E.COLI in complex with Z57299526”. X-ray diffraction, 1 ligand (WZD), 17 pockets (best druggability 0.75). MolNFT v1 #173651 on GenesisL1: 3D structure…
- PDB
- 7B6Q
- Type
- protein
- Length
- 954 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
- WZD
- Pockets
- 17 · best druggability 0.75
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 | 478 | 36% helix, 25% strand | P22188 |
| B | Udp-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6- diaminopimelate ligase (EC 6.3.2.13) | protein | 476 | 36% helix, 25% strand | P22188 |
Ligands and binding sites
- WZD · N-[(furan-2-yl)methyl]-1H-benzimidazol-2-amine · ligand · chains B
- IPA · Isopropyl alcohol · additive · chains 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 267 | 0.75 | 0.88 | 33 | empty |
| 2 | 259 | 0.74 | 0.88 | 37 | WZD, IPA |
| 3 | 743 | 0.72 | 0.78 | 66 | empty |
| 4 | 245 | 0.66 | 0.84 | 30 | empty |
| 5 | 256 | 0.66 | 0.83 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 424 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 7B6Q · PDBe 7B6Q · UniProt P22188
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