MolNFT v1 · #171590 · protein
Structure of the apo transcriptional repressor ATU1419 (vanr) from agrobacterium fabrum
6ZA7 · Transcriptional regulator, gntr family: “Structure of the apo transcriptional repressor ATU1419 (vanr) from agrobacterium fabrum”. X-ray diffraction, 2 ligands (ZN, SO4), 16 pockets (best druggability 0.86). MolNFT v1 #171590 on…
- PDB
- 6ZA7
- Type
- protein
- Length
- 948 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional regulator, gntr family
- UniProt
- A9CJ36
- Ligands
- ZN, SO4
- Pockets
- 16 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 67% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional regulator, gntr family | protein | 240 | 64% helix, 5% strand | A9CJ36 |
| B | Transcriptional regulator, gntr family | protein | 234 | 68% helix, 4% strand | A9CJ36 |
| C | Transcriptional regulator, gntr family | protein | 238 | 68% helix, 4% strand | A9CJ36 |
| D | Transcriptional regulator, gntr family | protein | 236 | 67% helix, 5% strand | A9CJ36 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · chains C
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 623 | 0.86 | 0.91 | 78 | PEG |
| 2 | 973 | 0.77 | 0.80 | 74 | empty |
| 3 | 608 | 0.76 | 0.83 | 60 | GOL |
| 4 | 890 | 0.75 | 0.79 | 70 | empty |
| 5 | 79 | 0.70 | 0.95 | 21 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1525 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 1476 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 607 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 505 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 292 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6ZA7 · Structure of the apo transcriptional repressor Atu1419 (VanR) from agrobacterium fabrum · 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 6ZA7 · PDBe 6ZA7 · UniProt A9CJ36
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