Research workbench
Structure of the two-component response regulator rcsb-DNA complex
Analyse Structure of the two-component response regulator rcsb-DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W43
- Type
- protein + DNA
- Length
- 440 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional regulatory protein rcsb; DNA (5'…
- UniProt
- P0DMC7
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional regulatory protein rcsb | protein | 202 | 49% helix, 14% strand | P0DMC7 |
| B | Transcriptional regulatory protein rcsb | protein | 194 | 46% helix, 13% strand | P0DMC7 |
| E | DNA (5'- D(*GP*AP*TP*TP*TP*AP*GP*GP*AP*AP*AP*AP*AP*TP*CP*TP*TP*AP*GP*AP*TP*A)- 3') | dna | 22 | — | — |
| F | DNA (5'- D(*TP*AP*TP*CP*TP*AP*AP*GP*AP*TP*TP*TP*TP*TP*CP*CP*TP*AP*AP*AP*TP*C)- 3') | dna | 22 | — | — |
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1060 | 0.76 | 0.78 | 87 | empty |
| 2 | 313 | 0.68 | 0.83 | 40 | empty |
| 3 | 156 | 0.47 | 0.77 | 19 | empty |
| 4 | 166 | 0.42 | 0.74 | 19 | empty |
| 5 | 59 | 0.37 | 0.79 | 14 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1109 Ų buried · 0 hydrogen bonds · protein-protein
- E–F · 951 Ų buried · 90 hydrogen bonds · nucleic-nucleic
- B–F · 453 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–E · 449 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–F · 367 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 5W43 · Structure of the two-component response regulator RcsB-DNA complex · the same entry in another collection · chain A against A, TM-score 1.00
- P0DMC7 · AlphaFold monomer V2.0 prediction for transcriptional regulatory protein rcsb (P0DMC7) · a predicted model of the same protein · chain A against A, TM-score 0.86
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 P0DMC7
- Elsewhere: RCSB PDB 5W43 · PDBe 5W43 · UniProt P0DMC7
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