MolNFT v1 · #8259 · protein
Crystal structure of the plasmid maintenance system EPSILON/ZETA: meachnism of toxin inactivation and toxin function
1GVN: “Crystal structure of the plasmid maintenance system EPSILON/ZETA: meachnism of toxin inactivation and toxin…”. X-ray diffraction, 1 ligand (SO4), 11 pockets (best druggability 0.83). MolNFT v1 #8259 on GenesisL1: 3D structure…
- PDB
- 1GVN
- Type
- protein
- Length
- 714 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epsilon; Zeta
- UniProt
- Q57231, Q54944
- Ligands
- SO4
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 61% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epsilon | protein | 87 | 74% helix, 0% strand | Q57231 |
| B | Zeta | protein | 272 | 56% helix, 10% strand | Q54944 |
| C | Epsilon | protein | 85 | 76% helix, 0% strand | Q57231 |
| D | Zeta | protein | 270 | 58% helix, 10% strand | Q54944 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 430 | 0.83 | 0.90 | 45 | empty |
| 2 | 401 | 0.82 | 0.91 | 37 | empty |
| 3 | 685 | 0.77 | 0.82 | 62 | SO4 |
| 4 | 694 | 0.75 | 0.81 | 65 | SO4 |
| 5 | 185 | 0.53 | 0.78 | 27 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1517 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1470 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1182 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1GVN · Crystal Structure of the Plasmid Maintenance System epsilon/zeta: Meachnism of toxin… · the same entry in another collection · chain D against D, TM-score 1.00
- Q54944 · AlphaFold monomer V2.0 prediction for toxin zeta (Q54944) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q57231 · AlphaFold monomer V2.0 prediction for antitoxin epsilon (Q57231) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 Q57231
- Every structure of UniProt Q54944
- Elsewhere: RCSB PDB 1GVN · PDBe 1GVN · UniProt Q57231 · UniProt Q54944
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