Research workbench
Streptomyces coelicolor ATP-loaded nrdr
Analyse Streptomyces coelicolor ATP-loaded nrdr in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7P37
- Type
- protein
- Length
- 1,764 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional repressor nrdr
- UniProt
- O69980
- Ligands
- ATP, ZN
- Pockets
- 17 · best druggability 0.76
Structure
electron microscopy · 1 distinct chain · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I, C, G, K, B, F, J, D, H, L | Transcriptional repressor nrdr | protein | 147 | 46% helix, 20% strand | O69980 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 24 copies · chains A, B, E, F, I, J, C, D, G, H, K, L
- ZN · Zinc ion · metal · 12 copies · chains A, E, I, C, G, K, B, F, J, D, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1182 | 0.76 | 0.79 | 90 | ATP |
| 2 | 1123 | 0.76 | 0.78 | 80 | ATP |
| 3 | 1197 | 0.75 | 0.78 | 86 | ATP |
| 4 | 1157 | 0.75 | 0.78 | 83 | ATP |
| 5 | 664 | 0.75 | 0.80 | 57 | ATP |
Interfaces
33 interfaces between chains.
- E–H · 1182 Ų buried · 19 hydrogen bonds · protein-protein
- I–L · 1180 Ų buried · 19 hydrogen bonds · protein-protein
- G–F · 1179 Ų buried · 19 hydrogen bonds · protein-protein
- K–J · 1179 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 1177 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 7P37 · Streptomyces coelicolor ATP-loaded NrdR · the same entry in another collection · chain L against L, 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 O69980
- Elsewhere: RCSB PDB 7P37 · PDBe 7P37 · UniProt O69980
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