MolNFT v1 · #173832 · protein + DNA
Crystal structure of the hth DNA binding protein ardk from R388 plasmid bound to IR3 DNA
7BCB · Kora domain-containing protein: “Crystal structure of the hth DNA binding protein ardk from R388 plasmid bound to IR3 DNA”. X-ray diffraction, 1 pocket (best druggability 0.67). MolNFT v1 #173832 on GenesisL1: 3D structure, binding…
- 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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