Research workbench
Crystal structure of transcriptional regulator (gntr family member) from pseudomonas syringae pv. tomato str. DC3000
Analyse Crystal structure of transcriptional regulator (gntr family member) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3C7J
- Type
- protein
- Length
- 464 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional regulator, gntr family
- UniProt
- Q87U60
- Ligands
- NI
- Pockets
- 8 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 73% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional regulator, gntr family | protein | 237 | 73% helix, 4% strand | Q87U60 |
| B | Transcriptional regulator, gntr family | protein | 227 | 73% helix, 4% strand | Q87U60 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 301 | 0.67 | 0.82 | 29 | empty |
| 2 | 466 | 0.60 | 0.75 | 35 | empty |
| 3 | 489 | 0.59 | 0.74 | 37 | empty |
| 4 | 214 | 0.54 | 0.78 | 23 | empty |
| 5 | 87 | 0.50 | 0.82 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1150 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 3C7J · Crystal structure of transcriptional regulator (GntR family member) from Pseudomonas… · 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 Q87U60
- Elsewhere: RCSB PDB 3C7J · PDBe 3C7J · UniProt Q87U60
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