Research workbench
The structure of the M60 catalytic domain from clostridium perfringens zmpc
Analyse The structure of the M60 catalytic domain from clostridium perfringens zmpc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XSZ
- Type
- protein
- Length
- 2,038 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Zmpc glycopeptidase
- UniProt
- F8UNJ8
- Ligands
- ZN
- Pockets
- 15 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Zmpc glycopeptidase | protein | 510 | 33% helix, 23% strand | F8UNJ8 |
| B, C | Zmpc glycopeptidase | protein | 509 | 33% helix, 23% strand | F8UNJ8 |
| D | Zmpc glycopeptidase | protein | 510 | 33% helix, 21% strand | F8UNJ8 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 23 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1117 | 0.77 | 0.79 | 108 | ZN, EDO |
| 2 | 1191 | 0.76 | 0.78 | 106 | ZN, EDO |
| 3 | 697 | 0.63 | 0.73 | 65 | empty |
| 4 | 224 | 0.51 | 0.76 | 35 | empty |
| 5 | 126 | 0.41 | 0.75 | 25 | empty |
Interfaces
4 interfaces between chains.
- A–D · 836 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 826 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 314 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 133 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6XSZ · The structure of the M60 catalytic domain from Clostridium perfringens ZmpC · 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 F8UNJ8
- Elsewhere: RCSB PDB 6XSZ · PDBe 6XSZ · UniProt F8UNJ8
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