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Crystal structure of a metallo-endopeptidases (BACOVA_00663) from bacteroides ovatus at 1.93 a resolution
Analyse Crystal structure of a metallo-endopeptidases (BACOVA_00663) from bacteroides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3P1V
- Type
- protein
- Length
- 810 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metallo-endopeptidase
- UniProt
- A7LS78
- Ligands
- ZN, K, PO4, CL
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metallo-endopeptidase | protein | 406 | 20% helix, 30% strand | A7LS78 |
| B | Metallo-endopeptidase | protein | 404 | 20% helix, 30% strand | A7LS78 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1058 | 0.84 | 0.85 | 114 | CL, PO4, PEG |
| 2 | 178 | 0.81 | 0.96 | 43 | empty |
| 3 | 128 | 0.80 | 0.98 | 26 | empty |
| 4 | 504 | 0.78 | 0.86 | 69 | CL, PO4, DMS |
| 5 | 566 | 0.76 | 0.83 | 61 | ZN, CL |
Interfaces
1 interface between chains.
- A–B · 1750 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 modified (engineered).
Compared structures
- 3P1V · Crystal structure of a metallo-endopeptidases (BACOVA_00663) from Bacteroides ovatus at… · 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 A7LS78
- Elsewhere: RCSB PDB 3P1V · PDBe 3P1V · UniProt A7LS78
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