Research workbench
BD0816 predatory endopeptidase from bdellovibrio bacteriovorus in complex with immunity protein BD3460
Analyse BD0816 predatory endopeptidase from bdellovibrio bacteriovorus in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CER
- Type
- protein
- Length
- 3,561 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BD0816; BD3460
- EC
- 3.4.16.4
- UniProt
- Q6MPN2, Q6MHS9
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, I | BD0816 (EC 3.4.16.4) | protein | 401 | 33% helix, 22% strand | Q6MPN2 |
| B, D, F, H, J, L | BD3460 | protein | 193 | 55% helix, 1% strand | Q6MHS9 |
| G | BD0816 (EC 3.4.16.4) | protein | 399 | 33% helix, 22% strand | Q6MPN2 |
| K | BD0816 (EC 3.4.16.4) | protein | 400 | 33% helix, 23% strand | Q6MPN2 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · chains G, H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1014 | 0.81 | 0.82 | 84 | empty |
| 2 | 786 | 0.81 | 0.84 | 75 | empty |
| 3 | 934 | 0.80 | 0.82 | 82 | empty |
| 4 | 1106 | 0.80 | 0.82 | 103 | empty |
| 5 | 742 | 0.79 | 0.83 | 100 | empty |
Interfaces
28 interfaces between chains.
- A–B · 1292 Ų buried · 27 hydrogen bonds · protein-protein
- G–H · 1275 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 1264 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1260 Ų buried · 25 hydrogen bonds · protein-protein
- K–L · 1259 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 5CER · Bd0816 Predatory Endopeptidase from Bdellovibrio bacteriovorus in complex with immunity… · 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 Q6MPN2
- Every structure of UniProt Q6MHS9
- Elsewhere: RCSB PDB 5CER · PDBe 5CER · UniProt Q6MPN2 · UniProt Q6MHS9
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