Research workbench

Streptomyces coelicolor DATP/ATP-loaded nrdr octamer

Analyse Streptomyces coelicolor DATP/ATP-loaded nrdr octamer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7P3Q
Type: protein
Length: 1,176 residues
Chains: 8
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transcriptional repressor nrdr
UniProt: O69980
Ligands: ATP, DTP, ZN
Pockets: 20 · best druggability 0.74

Structure

electron microscopy · 1 distinct chain · 46% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G, B, D, F, H	Transcriptional repressor nrdr	protein	147	46% helix, 20% strand	O69980

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 8 copies · chains A, C, E, H, G, F, B, D
DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
ZN · Zinc ion · metal · 8 copies · chains A, C, E, G, B, D, F, H

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	793	0.74	0.79	62	ATP, DTP
2	640	0.74	0.80	55	ATP, DTP
3	817	0.73	0.78	66	ATP, DTP
4	696	0.73	0.79	52	ATP, DTP
5	506	0.60	0.74	60	empty

Interfaces

18 interfaces between chains.

G–F · 1320 Å² buried · 28 hydrogen bonds · protein-protein
A–D · 1303 Å² buried · 26 hydrogen bonds · protein-protein
E–H · 1293 Å² buried · 25 hydrogen bonds · protein-protein
C–B · 1284 Å² buried · 21 hydrogen bonds · protein-protein
C–D · 951 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

7P3Q · Streptomyces coelicolor dATP/ATP-loaded NrdR octamer · the same entry in another collection · chain H against H, 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 0.72

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 7P3Q · PDBe 7P3Q · UniProt O69980

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