MolNFT v1 · #46577 · protein + DNA

NMR structure of the sigma-54 rpon domain bound to the-24 promoter element

2O8K · 5'-D(*TP*TP*TP*TP*GP*GP*CP*AP*CP*GP*TP*TP*TP*C)-3': “NMR structure of the sigma-54 rpon domain bound to the-24 promoter element”. Solution nmr, 2 pockets (best druggability 0.50). MolNFT v1 #46577 on GenesisL1: 3D structure, binding…

PDB: 2O8K
Type: protein + DNA
Length: 91 residues
Chains: 3
Method: solution nmr
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*TP*TP*TP*TP*GP*GP*CP*AP*CP*GP*TP*TP*TP*C)-3'…
UniProt: O66858
Pockets: 2 · best druggability 0.50

Structure

solution nmr · 3 distinct chains · 54% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	5'-D(TPTPTPTPGPGPCPAPCPGPTPTPTPC)-3'	dna	14	—	—
C	5'-D(GPAPAPAPCPGPTPGPCPCPAPAPAPA)-3'	dna	14	—	—
A	RNA polymerase sigma factor rpon	protein	63	54% helix, 0% strand	O66858

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	225	0.50	0.76	16	empty
2	50	0.44	0.84	14	empty

Interfaces

3 interfaces between chains.

B–C · 646 Å² buried · 67 hydrogen bonds · nucleic-nucleic
C–A · 426 Å² buried · 12 hydrogen bonds · protein-nucleic
B–A · 418 Å² buried · 14 hydrogen bonds · protein-nucleic

Compared structures

2O8K · NMR Structure of the Sigma-54 RpoN Domain Bound to the-24 Promoter Element · the same entry in another collection · chain B against B, 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 O66858
Elsewhere: RCSB PDB 2O8K · PDBe 2O8K · UniProt O66858

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