Research workbench
Structure of the transcriptional repressor ATU1419 (vanr) in complex with a fortuitous citrate from agrobacterium fabrum
Analyse Structure of the transcriptional repressor ATU1419 (vanr) in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Z74
- Type
- protein
- Length
- 942 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional regulator, gntr family
- UniProt
- A9CJ36
- Ligands
- ZN, NA, SO4
- Pockets
- 13 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 66% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional regulator, gntr family | protein | 237 | 66% helix, 5% strand | A9CJ36 |
| B | Transcriptional regulator, gntr family | protein | 238 | 67% helix, 5% strand | A9CJ36 |
| C | Transcriptional regulator, gntr family | protein | 232 | 66% helix, 5% strand | A9CJ36 |
| D | Transcriptional regulator, gntr family | protein | 235 | 66% helix, 5% strand | A9CJ36 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 2 copies · chains D
- SO4 · Sulfate ion · ion · chains B
- EDO · 1,2-ethanediol · additive · 23 copies · chains A, D, B, C
- CIT · Citric acid · additive · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 412 | 0.84 | 0.93 | 57 | EDO |
| 2 | 72 | 0.76 | 0.99 | 25 | CIT |
| 3 | 893 | 0.74 | 0.78 | 74 | EDO |
| 4 | 834 | 0.73 | 0.78 | 78 | GOL, EDO |
| 5 | 261 | 0.52 | 0.75 | 37 | EDO |
Interfaces
6 interfaces between chains.
- C–D · 1534 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1530 Ų buried · 31 hydrogen bonds · protein-protein
- A–D · 767 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 631 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 284 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6Z74 · 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 6Z74 · PDBe 6Z74 · UniProt A9CJ36
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