Research workbench
BD3459 predatory endopeptidase from bdellovibrio bacteriovorus, K38M form
Analyse BD3459 predatory endopeptidase from bdellovibrio bacteriovorus, K38M form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CEB
- Type
- protein
- Length
- 770 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BD3459
- EC
- 3.4.16.4
- UniProt
- Q6MHT0
- Pockets
- 13 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | BD3459 (EC 3.4.16.4) | protein | 387 | 35% helix, 21% strand | Q6MHT0 |
| B | BD3459 (EC 3.4.16.4) | protein | 383 | 35% helix, 22% strand | Q6MHT0 |
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 202 | 0.61 | 0.82 | 37 | empty |
| 2 | 191 | 0.51 | 0.77 | 31 | empty |
| 3 | 179 | 0.50 | 0.77 | 28 | empty |
| 4 | 127 | 0.47 | 0.78 | 24 | empty |
| 5 | 74 | 0.35 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 708 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
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 Q6MHT0
- Elsewhere: RCSB PDB 5CEB · PDBe 5CEB · UniProt Q6MHT0
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