MolNFT v1 · #174522 · protein
Toxin-antitoxin complex from klebsiella pneumoniae
7BY3 · Copg family transcriptional regulator: “Toxin-antitoxin complex from klebsiella pneumoniae”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.77). MolNFT v1 #174522 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7BY3
- Type
- protein
- Length
- 372 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Copg family transcriptional regulator; Ribonuclease vapc
- EC
- 3.1.-.-
- UniProt
- W9BQC4, A0A0W8AM92
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Copg family transcriptional regulator | protein | 64 | 63% helix, 0% strand | W9BQC4 |
| B, D | Ribonuclease vapc (EC 3.1.-.-) | protein | 122 | 54% helix, 12% strand | A0A0W8AM92 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 78 | 0.77 | 0.99 | 21 | SO4 |
| 2 | 71 | 0.56 | 0.87 | 21 | empty |
| 3 | 97 | 0.56 | 0.85 | 21 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1397 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1394 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 1023 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 237 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 163 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7BY3 · Toxin-antitoxin complex from klebsiella pneumoniae · 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 W9BQC4
- Every structure of UniProt A0A0W8AM92
- Elsewhere: RCSB PDB 7BY3 · PDBe 7BY3 · UniProt W9BQC4 · UniProt A0A0W8AM92
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