Research workbench
The crystal structure of peptidoglycan peptidase in complex with inhibitor 2-1
Analyse The crystal structure of peptidoglycan peptidase in complex with inhibitor 2-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7E63
- 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
- HY9, ZN
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 12% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peptidase M23 | protein | 255 | 12% helix, 40% strand | A0A1J6PWI8 |
Ligands and binding sites
- HY9 · 2-[[(3S)-3-acetamido-4-[[(2R)-1-(oxidanylamino)-1-oxidanylidene-propan-2-yl]amino]-4-oxidanylidene-butyl]-(cyclopentylmethyl)amino]ethanoic acid · ligand · chains B
- 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
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1035 | 0.75 | 0.78 | 105 | empty |
| 2 | 443 | 0.60 | 0.75 | 35 | empty |
| 3 | 406 | 0.59 | 0.75 | 34 | HY9 |
| 4 | 160 | 0.54 | 0.79 | 27 | empty |
| 5 | 59 | 0.30 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 662 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7E63 · The crystal structure of peptidoglycan peptidase in complex with inhibitor 2-1 · 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 7E63 · PDBe 7E63 · UniProt A0A1J6PWI8
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