MolNFT v1 · #177057 · protein
The crystal structure of peptidoglycan peptidase in complex with inhibitor 3
7E65 · Peptidase M23: “The crystal structure of peptidoglycan peptidase in complex with inhibitor 3”. X-ray diffraction, 2 ligands (HXO, ZN), 6 pockets (best druggability 0.71). MolNFT v1 #177057 on GenesisL1: 3D structure, binding sites…
- PDB
- 7E65
- Type
- protein
- Length
- 510 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidase M23
- UniProt
- A0A1J6PWI8
- Ligands
- HXO, ZN
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 12% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peptidase M23 | protein | 255 | 12% helix, 43% strand | A0A1J6PWI8 |
Ligands and binding sites
- HXO · (2S)-2-acetamido-N-[(2R)-1-(oxidanylamino)-1-oxidanylidene-propan-2-yl]-3-(4-sulfamoylphenyl) propanamide · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 797 | 0.71 | 0.77 | 69 | empty |
| 2 | 439 | 0.62 | 0.76 | 33 | HXO |
| 3 | 64 | 0.62 | 0.92 | 20 | empty |
| 4 | 464 | 0.61 | 0.75 | 37 | empty |
| 5 | 132 | 0.48 | 0.78 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 724 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7E65 · The crystal structure of peptidoglycan peptidase in complex with inhibitor 3 · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A1J6PWI8
- Elsewhere: RCSB PDB 7E65 · PDBe 7E65 · UniProt A0A1J6PWI8
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