Research workbench
Crystal structure of the lanthipeptide zinc-metallopeptidase eryp from saccharopolyspora erythraea in intermediate state
Analyse Crystal structure of the lanthipeptide zinc-metallopeptidase eryp from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7V9P
- Type
- protein
- Length
- 1,695 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alanine aminopeptidase
- EC
- 3.4.11.2
- UniProt
- A4F9D7
- Ligands
- ZN
- Pockets
- 18 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alanine aminopeptidase (EC 3.4.11.2) | protein | 850 | 45% helix, 22% strand | A4F9D7 |
| B | Alanine aminopeptidase (EC 3.4.11.2) | protein | 845 | 44% helix, 22% strand | A4F9D7 |
Ligands and binding sites
- 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
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 837 | 0.79 | 0.82 | 93 | empty |
| 2 | 1166 | 0.76 | 0.78 | 109 | empty |
| 3 | 936 | 0.75 | 0.78 | 91 | empty |
| 4 | 511 | 0.71 | 0.80 | 46 | empty |
| 5 | 314 | 0.58 | 0.77 | 42 | empty |
Interfaces
1 interface between chains.
- A–B · 1305 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 7V9P · Crystal structure of the lanthipeptide zinc-metallopeptidase EryP from saccharopolyspora… · 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 A4F9D7
- Elsewhere: RCSB PDB 7V9P · PDBe 7V9P · UniProt A4F9D7
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