Research workbench
Crystal structure of the hth DNA binding protein ardk from R388 plasmid bound to IR3 DNA
Analyse Crystal structure of the hth DNA binding protein ardk from R388 plasmid bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BCB
- Type
- protein + DNA
- Length
- 227 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kora domain-containing protein; DNA (5'- D(*TP*AP*AP*TP*GP*TP*CP*AP*AP*AP*TP*AP*TP*TP*GP*A…
- UniProt
- Q6I6B7
- Pockets
- 1 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 64% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Kora domain-containing protein | protein | 94 | 64% helix, 7% strand | Q6I6B7 |
| B | Kora domain-containing protein | protein | 97 | 64% helix, 7% strand | Q6I6B7 |
| C | DNA (5'- D(*TP*AP*AP*TP*GP*TP*CP*AP*AP*AP*TP*AP*TP*TP*GP*AP*CP*A)-3') | dna | 18 | — | — |
| D | DNA (5'- D(*TP*GP*TP*CP*AP*AP*TP*AP*TP*TP*TP*GP*AP*CP*AP*TP*TP*A)-3') | dna | 18 | — | — |
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 827 | 0.67 | 0.75 | 64 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1336 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 777 Ų buried · 61 hydrogen bonds · nucleic-nucleic
- B–D · 418 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–C · 417 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–C · 409 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
- 7BCB · Crystal structure of the HTH DNA binding protein ArdK from R388 plasmid bound to IR3 DNA · 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 Q6I6B7
- Elsewhere: RCSB PDB 7BCB · PDBe 7BCB · UniProt Q6I6B7
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