Research workbench
Streptomyces coelicolor DATP/ATP-loaded nrdr in complex with its cognate DNA
Analyse Streptomyces coelicolor DATP/ATP-loaded nrdr in complex with its cognate DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7P3F
- Type
- protein + DNA
- Length
- 688 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional repressor nrdr; DNA (50-mer)
- UniProt
- O69980
- Ligands
- ATP, DTP, ZN
- Pockets
- 15 · best druggability 0.72
Structure
electron microscopy · 3 distinct chains · 44% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, B, D | Transcriptional repressor nrdr | protein | 147 | 44% helix, 22% strand | O69980 |
| F | DNA (50-mer) | dna | 50 | — | — |
| R | DNA (50-mer) | dna | 50 | — | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, C, B, D
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 768 | 0.72 | 0.77 | 63 | ATP, DTP |
| 2 | 649 | 0.71 | 0.78 | 47 | ATP, DTP |
| 3 | 435 | 0.56 | 0.73 | 46 | empty |
| 4 | 350 | 0.53 | 0.74 | 37 | empty |
| 5 | 132 | 0.50 | 0.80 | 26 | empty |
Interfaces
13 interfaces between chains.
- F–R · 2561 Ų buried · 252 hydrogen bonds · nucleic-nucleic
- C–B · 1279 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 1278 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 925 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 921 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7P3F · Streptomyces coelicolor dATP/ATP-loaded NrdR in complex with its cognate DNA · the same entry in another collection · chain B against B, TM-score 1.00
- O69980 · AlphaFold monomer V2.0 prediction for transcriptional repressor nrdr (O69980) · a predicted model of the same protein · chain A against A, TM-score 0.75
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 O69980
- Elsewhere: RCSB PDB 7P3F · PDBe 7P3F · UniProt O69980
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.