MolNFT v1 · #189395 · protein + DNA
C-terminal domain of vrar
7VE5 · DNA-binding response regulator: “C-terminal domain of vrar”. X-ray diffraction, 1 ligand (MG), 2 pockets (best druggability 0.65). MolNFT v1 #189395 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7VE5
- Type
- protein + DNA
- Length
- 170 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-binding response regulator; R1-DNA
- UniProt
- A0A1Q8DEZ3
- Ligands
- MG
- Pockets
- 2 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA-binding response regulator | protein | 66 | 70% helix, 0% strand | A0A1Q8DEZ3 |
| C | R1-DNA | dna | 19 | — | — |
| D | R1-DNA | dna | 19 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 489 | 0.65 | 0.78 | 55 | MG |
| 2 | 70 | 0.30 | 0.74 | 14 | empty |
Interfaces
6 interfaces between chains.
- C–D · 836 Ų buried · 74 hydrogen bonds · nucleic-nucleic
- A–B · 483 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 456 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–C · 332 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–D · 316 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 7VE5 · C-terminal domain of VraR · 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 A0A1Q8DEZ3
- Elsewhere: RCSB PDB 7VE5 · PDBe 7VE5 · UniProt A0A1Q8DEZ3
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