Research workbench
Crystal structure of kora bound to operator DNA: insight into repressor cooperation in RP4 gene regulation
Analyse Crystal structure of kora bound to operator DNA: insight into repressor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2W7N
- Type
- protein + DNA
- Length
- 261 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trfb transcriptional repressor protein; 5'-D(*AP*AP*TP*GP*TP*TP*TP*AP*GP*CP…
- UniProt
- P03052
- Pockets
- 1 · best druggability 0.59
Structure
x-ray diffraction · 4 distinct chains · 65% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trfb transcriptional repressor protein | protein | 94 | 64% helix, 9% strand | P03052 |
| B | Trfb transcriptional repressor protein | protein | 95 | 66% helix, 8% strand | P03052 |
| E, G | 5'-D(*AP*AP*TP*GP*TP*TP*TP*AP*GP*CP *TP*AP*AP*AP*CP*AP*AP*G)-3' | dna | 18 | — | — |
| F, H | 5'-D(*CP*BRUP*BRUP*GP*TP*TP*TP*AP*GP*CP*TP*AP *AP*AP*CP*AP*BRUP*T)-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 | 413 | 0.59 | 0.75 | 76 | empty |
Interfaces
15 interfaces between chains.
- F–G · 1994 Ų buried · 736 hydrogen bonds · nucleic-nucleic
- E–H · 1983 Ų buried · 737 hydrogen bonds · nucleic-nucleic
- A–B · 1084 Ų buried · 16 hydrogen bonds · protein-protein
- E–G · 812 Ų buried · 85 hydrogen bonds · nucleic-nucleic
- E–F · 792 Ų buried · 84 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 6 modified (nucleotide modification).
Compared structures
- 2W7N · Crystal Structure of KorA Bound to Operator DNA: Insight into Repressor Cooperation in… · the same entry in another collection · chain G against G, TM-score 1.00
- P03052 · AlphaFold monomer V2.0 prediction for trfb transcriptional repressor protein (P03052) · a predicted model of the same protein · chain A against A, TM-score 0.84
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 P03052
- Elsewhere: RCSB PDB 2W7N · PDBe 2W7N · UniProt P03052
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