MolNFT v1 · #171862 · protein + DNA
Structure of rcsb from salmonella enterica serovar typhimurium bound to promoter rpra in the presence of phosphomimetic BEF3-
6ZJ2 · Transcriptional regulatory protein rcsb: “Structure of rcsb from salmonella enterica serovar typhimurium bound to promoter rpra in the presence of…”. X-ray diffraction, 2 ligands (BFD, MG), 20 pockets (best druggability 0.77).…
- PDB
- 6ZJ2
- Type
- protein + DNA
- Length
- 1,543 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional regulatory protein rcsb; Rpra promoter sequence; DNA (5'…
- UniProt
- P58663
- Ligands
- BFD, MG
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 10 distinct chains · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Transcriptional regulatory protein rcsb | protein | 208 | 48% helix, 11% strand | P58663 |
| A | Transcriptional regulatory protein rcsb | protein | 202 | 49% helix, 13% strand | P58663 |
| D | Transcriptional regulatory protein rcsb | protein | 201 | 50% helix, 12% strand | P58663 |
| C | Transcriptional regulatory protein rcsb | protein | 198 | 50% helix, 12% strand | P58663 |
| E, G | Rpra promoter sequence | dna | 22 | — | — |
| F, I | DNA (5'- D(P*CP*CP*GP*AP*TP*CP*AP*GP*AP*TP*TP*CP*GP*TP*CP*TP*CP*AP*AP*TP*AP*GP *G)-3') | dna | 22 | — | — |
| L | Transcriptional regulatory protein rcsb | protein | 166 | 48% helix, 11% strand | P58663 |
| M | Transcriptional regulatory protein rcsb | protein | 179 | 46% helix, 15% strand | P58663 |
| N | Transcriptional regulatory protein rcsb | protein | 178 | 47% helix, 12% strand | P58663 |
| O | Transcriptional regulatory protein rcsb | protein | 123 | 38% helix, 22% strand | P58663 |
Ligands and binding sites
- BFD · Aspartate beryllium trifluoride · ligand · 2 copies · chains B, A
- MG · Magnesium ion · metal · 4 copies · chains B, A, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 919 | 0.77 | 0.80 | 87 | BFD, MG |
| 2 | 984 | 0.77 | 0.79 | 80 | MG |
| 3 | 592 | 0.76 | 0.83 | 82 | empty |
| 4 | 924 | 0.72 | 0.76 | 97 | empty |
| 5 | 879 | 0.72 | 0.76 | 77 | empty |
Interfaces
24 interfaces between chains.
- E–F · 962 Ų buried · 83 hydrogen bonds · nucleic-nucleic
- G–I · 957 Ų buried · 86 hydrogen bonds · nucleic-nucleic
- D–C · 911 Ų buried · 2 hydrogen bonds · protein-protein
- B–A · 853 Ų buried · 1 hydrogen bond · protein-protein
- L–M · 656 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6ZJ2 · Structure of RcsB from Salmonella enterica serovar Typhimurium bound to promoter rprA in… · the same entry in another collection · chain O against O, 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 P58663
- Elsewhere: RCSB PDB 6ZJ2 · PDBe 6ZJ2 · UniProt P58663
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