Research workbench
Crystal structure of the hth DNA binding protein ardk from R388 plasmid bound to a direct-repeat DNA element
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
- 7BCA
- 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*GP*TP*CP*AP*AP*TP*AP*GP*GP*TP*GP*TP*CP*AP*A…
- UniProt
- Q6I6B7
- Pockets
- 2 · best druggability 0.69
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 | 96 | 64% helix, 7% strand | Q6I6B7 |
| B | Kora domain-containing protein | protein | 93 | 65% helix, 8% strand | Q6I6B7 |
| C | DNA (5'- D(*TP*GP*TP*CP*AP*AP*TP*AP*GP*GP*TP*GP*TP*CP*AP*AP*TP*AP*C)-3') | dna | 19 | — | — |
| D | DNA (5'- D(*GP*TP*AP*TP*TP*GP*AP*CP*AP*CP*CP*TP*AP*TP*TP*GP*AP*CP*A)-3') | dna | 19 | — | — |
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 850 | 0.69 | 0.76 | 59 | empty |
| 2 | 216 | 0.59 | 0.81 | 21 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1368 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 872 Ų buried · 79 hydrogen bonds · nucleic-nucleic
- A–C · 447 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–D · 446 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–D · 441 Ų buried · 13 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 7BCA · Crystal structure of the HTH DNA binding protein ArdK from R388 plasmid bound to a… · 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 7BCA · PDBe 7BCA · UniProt Q6I6B7
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