MolNFT v1 · #115262 · protein
BD3459 predatory endopeptidase from bdellovibrio bacteriovorus in complex with immunity protein BD3460
5CEC: “BD3459 predatory endopeptidase from bdellovibrio bacteriovorus in complex with immunity protein BD3460”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.77). MolNFT v1 #115262 on GenesisL1: 3D structure, binding…
- PDB
- 5CEC
- Type
- protein
- Length
- 594 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BD3459; BD3460
- EC
- 3.4.16.4
- UniProt
- Q6MHT0, Q6MHS9
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | BD3459 (EC 3.4.16.4) | protein | 401 | 34% helix, 21% strand | Q6MHT0 |
| B | BD3460 | protein | 193 | 54% helix, 1% strand | Q6MHS9 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1082 | 0.77 | 0.80 | 86 | SO4 |
| 2 | 123 | 0.45 | 0.77 | 28 | empty |
| 3 | 99 | 0.45 | 0.79 | 23 | empty |
| 4 | 63 | 0.35 | 0.78 | 15 | empty |
| 5 | 78 | 0.35 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1221 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5CEC · Bd3459 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 Q6MHT0
- Every structure of UniProt Q6MHS9
- Elsewhere: RCSB PDB 5CEC · PDBe 5CEC · UniProt Q6MHT0 · UniProt Q6MHS9
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