Research workbench
Crystal structure of the P22 C2 repressor protein in complex with synthetic operator 9C in the presence of rb+
Analyse Crystal structure of the P22 C2 repressor protein in complex with synthetic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JXD
- Type
- protein + DNA
- Length
- 172 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*AP*TP*TP*TP*AP*AP*GP*AP*CP*GP*TP*CP*TP*TP*AP*AP*AP *TP*G)-3'; Repressor protein…
- UniProt
- P69202
- Ligands
- RB
- Pockets
- 1 · best druggability 0.29
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 5'-D(*CP*AP*TP*TP*TP*AP*AP*GP*AP*CP*GP*TP*CP*TP*TP*AP*AP*AP *TP*G)-3' | dna | 20 | — | — |
| L, R | Repressor protein C2 | protein | 66 | 68% helix, 2% strand | P69202 |
Ligands and binding sites
- RB · Rubidium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 58 | 0.29 | 0.75 | 13 | empty |
Interfaces
6 interfaces between chains.
- A–B · 931 Ų buried · 85 hydrogen bonds · nucleic-nucleic
- L–R · 406 Ų buried · 5 hydrogen bonds · protein-protein
- B–R · 392 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–L · 382 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–L · 354 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
- 3JXD · Crystal structure of the P22 c2 repressor protein in complex with synthetic operator 9C… · 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 P69202
- Elsewhere: RCSB PDB 3JXD · PDBe 3JXD · UniProt P69202
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