Research workbench
Structure of two rcsb dimers bound to two parallel dnas.
Analyse Structure of two rcsb dimers bound to two parallel dnas. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VXN
- Type
- protein + DNA
- Length
- 864 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional regulatory protein rcsb; DNA (5'…
- UniProt
- P0DMC7
- Pockets
- 14 · best druggability 0.80
Structure
x-ray diffraction · 6 distinct chains · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional regulatory protein rcsb | protein | 201 | 48% helix, 13% strand | P0DMC7 |
| B | Transcriptional regulatory protein rcsb | protein | 191 | 47% helix, 14% strand | P0DMC7 |
| E, G | DNA (5'- D(*TP*TP*TP*AP*GP*GP*AP*AP*AP*AP*AP*TP*CP*TP*TP*AP*GP*A)-3') | dna | 18 | — | — |
| F, H | 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 | 18 | — | — |
| C | Transcriptional regulatory protein rcsb | protein | 203 | 47% helix, 13% strand | P0DMC7 |
| D | Transcriptional regulatory protein rcsb | protein | 197 | 47% helix, 12% strand | P0DMC7 |
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 973 | 0.80 | 0.82 | 86 | empty |
| 2 | 1035 | 0.76 | 0.79 | 74 | empty |
| 3 | 595 | 0.73 | 0.81 | 50 | empty |
| 4 | 432 | 0.72 | 0.83 | 39 | empty |
| 5 | 282 | 0.59 | 0.78 | 40 | empty |
Interfaces
17 interfaces between chains.
- C–D · 1020 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 943 Ų buried · 1 hydrogen bond · protein-protein
- E–F · 770 Ų buried · 51 hydrogen bonds · nucleic-nucleic
- G–H · 766 Ų buried · 50 hydrogen bonds · nucleic-nucleic
- B–F · 401 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
- 5VXN · Structure of two RcsB dimers bound to two parallel DNAs. · the same entry in another collection · chain H against H, 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 5VXN · PDBe 5VXN · UniProt P0DMC7
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