MolNFT v1 · #153711 · protein
Structure of H247A mutant peptidoglycan peptidase complex with penta peptide
6JN1 · Peptidase M23: “Structure of H247A mutant peptidoglycan peptidase complex with penta peptide”. X-ray diffraction, 2 ligands (C0O, ZN), 2 pockets (best druggability 0.58). MolNFT v1 #153711 on GenesisL1: 3D structure, binding sites…
- PDB
- 6JN1
- Type
- protein
- Length
- 256 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidase M23; C0O-dal-dal
- UniProt
- A0A1J6PWI8
- Ligands
- C0O, ZN
- Pockets
- 2 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidase M23 | protein | 254 | 12% helix, 42% strand | A0A1J6PWI8 |
| B | C0O-dal-dal | protein | 2 | 0% helix, 0% strand | — |
Ligands and binding sites
- C0O · (~{Z},2~{R},6~{S})-2,6-bis(azanyl)hept-3-enedioic acid · ligand · chains A, B
- ZN · Zinc ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 303 | 0.58 | 0.77 | 25 | C0O |
| 2 | 140 | 0.52 | 0.80 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 173 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 d-amino, 1 covalent (D-amino acid, covalent ligand).
Compared structures
- 6JN1 · Structure of H247A mutant peptidoglycan peptidase complex with penta peptide · 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 6JN1 · PDBe 6JN1 · UniProt A0A1J6PWI8
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