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Crystal structure of co-catalytic metallopeptidase (YP_387682.1) from desulfovibrio desulfuricans G20 at 1.60 a resolution
Analyse Crystal structure of co-catalytic metallopeptidase (YP_387682.1) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2RB7
- Type
- protein
- Length
- 720 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidase, M20/M25/M40 family
- UniProt
- Q313A9
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peptidase, M20/M25/M40 family | protein | 360 | 36% helix, 29% strand | Q313A9 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B
- PGE · Triethylene glycol · additive · chains A
- PG4 · Tetraethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 382 | 0.73 | 0.84 | 47 | empty |
| 2 | 470 | 0.71 | 0.81 | 57 | empty |
| 3 | 154 | 0.47 | 0.77 | 20 | empty |
| 4 | 165 | 0.45 | 0.75 | 21 | empty |
| 5 | 165 | 0.44 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1770 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (engineered).
Compared structures
- 2RB7 · Crystal structure of co-catalytic metallopeptidase (YP_387682.1) from Desulfovibrio… · 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 Q313A9
- Elsewhere: RCSB PDB 2RB7 · PDBe 2RB7 · UniProt Q313A9
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