Research workbench
Structure of open form of peptidoglycan peptidase
Analyse Structure of open form of peptidoglycan peptidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JMX
- Type
- protein
- Length
- 256 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidase M23
- UniProt
- A0A1J6PWI8
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 12% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidase M23 | protein | 256 | 12% helix, 42% strand | A0A1J6PWI8 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
- GOL · Glycerol · additive · 3 copies · chains A
- TAR · D(-)-tartaric acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 338 | 0.56 | 0.75 | 26 | ZN, TAR, GOL |
| 2 | 141 | 0.47 | 0.77 | 26 | empty |
Compared structures
- 6JMX · Structure of open form of peptidoglycan peptidase · 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 6JMX · PDBe 6JMX · UniProt A0A1J6PWI8
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