Research workbench
Structure of the transcriptional repressor ATU1419 (vanr) from agrobacterium fabrum in complex a palindromic DNA (C2221 space group)
Analyse Structure of the transcriptional repressor ATU1419 (vanr) from agrobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZA3
- Type
- protein + DNA
- Length
- 497 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional regulator, gntr family; DNA (5'-D(*AP*TP*GP*TP*AP*TP*AP*CP*AP*T)-3')
- UniProt
- A9CJ36
- Ligands
- ZN, CL
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 65% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional regulator, gntr family | protein | 238 | 65% helix, 4% strand | A9CJ36 |
| B | Transcriptional regulator, gntr family | protein | 239 | 66% helix, 4% strand | A9CJ36 |
| E, F | DNA (5'-D(*AP*TP*GP*TP*AP*TP*AP*CP*AP*T)-3') | dna | 10 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B, F
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains B
- ACT · Acetate ion · additive · chains B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 322 | 0.68 | 0.82 | 42 | empty |
| 2 | 55 | 0.66 | 0.95 | 15 | empty |
| 3 | 162 | 0.42 | 0.74 | 16 | EDO |
| 4 | 50 | 0.39 | 0.82 | 18 | empty |
| 5 | 51 | 0.35 | 0.80 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1493 Ų buried · 35 hydrogen bonds · protein-protein
- E–F · 446 Ų buried · 41 hydrogen bonds · nucleic-nucleic
- B–E · 330 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–F · 322 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–F · 308 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 6ZA3 · Structure of the transcriptional repressor Atu1419 (VanR) from agrobacterium fabrum in… · 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 A9CJ36
- Elsewhere: RCSB PDB 6ZA3 · PDBe 6ZA3 · UniProt A9CJ36
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