MolNFT v1 · #171583 · protein
Structure of the transcriptional repressor ATU1419 (vanr) in complex with a fortuitous citrate from agrobacterium fabrum (P21212 space group)
6ZA0 · Transcriptional regulator, gntr family: “Structure of the transcriptional repressor ATU1419 (vanr) in complex with a fortuitous citrate from…”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.73). MolNFT v1 #171583…
- PDB
- 6ZA0
- Type
- protein
- Length
- 477 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional regulator, gntr family
- UniProt
- A9CJ36
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 67% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional regulator, gntr family | protein | 240 | 65% helix, 5% strand | A9CJ36 |
| B | Transcriptional regulator, gntr family | protein | 237 | 68% helix, 4% strand | A9CJ36 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CIT · Citric acid · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 60 | 0.73 | 0.99 | 21 | CIT |
| 2 | 369 | 0.58 | 0.76 | 34 | empty |
| 3 | 205 | 0.46 | 0.74 | 24 | empty |
| 4 | 77 | 0.46 | 0.81 | 15 | empty |
| 5 | 56 | 0.34 | 0.78 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1627 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 6ZA0 · Structure of the transcriptional repressor Atu1419 (VanR) in complex with a fortuitous… · 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 6ZA0 · PDBe 6ZA0 · UniProt A9CJ36
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