Research workbench
Crystal structure of rsp in complex with beta-NAD+ and operator DNA
Analyse Crystal structure of rsp in complex with beta-NAD+ and operator DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WGI
- Type
- protein + DNA
- Length
- 964 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Redox-sensing transcriptional repressor rex; DNA (5'…
- UniProt
- D5KM69
- Ligands
- NAJ
- Pockets
- 16 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Redox-sensing transcriptional repressor rex | protein | 217 | 47% helix, 18% strand | D5KM69 |
| E, F, G, H | DNA (5'- D(*TP*AP*GP*AP*TP*TP*GP*TP*TP*AP*AP*TP*CP*GP*AP*TP*TP*AP*AP*CP*AP*AP* TP*C)-3') | dna | 24 | — | — |
Ligands and binding sites
- NAJ · Nicotinamide-adenine-dinucleotide (acidic form) · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1187 | 0.75 | 0.78 | 121 | NAJ |
| 2 | 664 | 0.72 | 0.78 | 79 | NAJ |
| 3 | 809 | 0.67 | 0.75 | 57 | empty |
| 4 | 784 | 0.67 | 0.74 | 45 | empty |
| 5 | 415 | 0.61 | 0.76 | 40 | empty |
Interfaces
14 interfaces between chains.
- C–D · 2906 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 2896 Ų buried · 34 hydrogen bonds · protein-protein
- G–H · 1058 Ų buried · 87 hydrogen bonds · nucleic-nucleic
- E–F · 1045 Ų buried · 90 hydrogen bonds · nucleic-nucleic
- D–H · 522 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 3WGI · Crystal structure of RSP in complex with beta-NAD+ and operator DNA · the same entry in another collection · chain G against G, 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 D5KM69
- Elsewhere: RCSB PDB 3WGI · PDBe 3WGI · UniProt D5KM69
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