MolNFT v1 · #71666 · protein + DNA

Structure of SOPB(155-323)-18MER DNA complex, I23 form

3MKY · DNA (5'- D(*CP*TP*GP*GP*GP*AP*CP*CP*AP*TP*GP*GP*TP*CP*CP*CP*…: “Structure of SOPB(155-323)-18MER DNA complex, I23 form”. X-ray diffraction, 1 ligand (SO4), 2 pockets (best druggability 0.45). MolNFT v1 #71666 on GenesisL1: 3D…

PDB: 3MKY
Type: protein + DNA
Length: 265 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'- D(*CP*TP*GP*GP*GP*AP*CP*CP*AP*TP*GP*GP*TP*CP*CP*CP*AP*G)-3'); Protein sopb
UniProt: P62558
Ligands: SO4
Pockets: 2 · best druggability 0.45

Structure

x-ray diffraction · 3 distinct chains · 68% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
U, T	DNA (5'- D(CPTPGPGPGPAPCPCPAPTPGPGPTPCPCPCPAPG)-3')	dna	18	—	—
B	Protein sopb	protein	115	70% helix, 0% strand	P62558
P	Protein sopb	protein	114	67% helix, 0% strand	P62558

Ligands and binding sites

SO4 · Sulfate ion · ion · 10 copies · chains B, U, T, P

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	146	0.45	0.77	26	empty
2	83	0.31	0.73	21	empty

Interfaces

4 interfaces between chains.

U–T · 821 Å² buried · 94 hydrogen bonds · nucleic-nucleic
B–P · 724 Å² buried · 14 hydrogen bonds · protein-protein
T–B · 472 Å² buried · 14 hydrogen bonds · protein-nucleic
U–B · 364 Å² buried · 11 hydrogen bonds · protein-nucleic

Compared structures

3MKY · Structure of SopB(155-323)-18mer DNA complex, I23 form · the same entry in another collection · chain U against U, TM-score 1.00
P62558 · AlphaFold monomer V2.0 prediction for protein sopb (P62558) · a predicted model of the same protein · chain P against A, TM-score 0.95

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 P62558
Elsewhere: RCSB PDB 3MKY · PDBe 3MKY · UniProt P62558

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