MolNFT v1 · #76525 · protein

Crystal structure of the substrate binding domain of E.COLI dnak in complex with the antimicrobial peptide oncocin

3QNJ · Chaperone protein dnak: “Crystal structure of the substrate binding domain of E.COLI dnak in complex with the antimicrobial peptide…”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.77). MolNFT v1 #76525 on…

PDB: 3QNJ
Type: protein
Length: 433 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chaperone protein dnak; Antimicrobial peptide oncocin
UniProt: P0A6Y8
Ligands: SO4
Pockets: 6 · best druggability 0.77

Structure

x-ray diffraction · 4 distinct chains · 35% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Chaperone protein dnak	protein	204	34% helix, 28% strand	P0A6Y8
B	Chaperone protein dnak	protein	211	39% helix, 29% strand	P0A6Y8
C	Antimicrobial peptide oncocin	protein	8	0% helix, 13% strand	—
D	Antimicrobial peptide oncocin	protein	10	0% helix, 20% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 6 copies · chains A, B, D, C

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

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	929	0.77	0.80	69	SO4
2	698	0.76	0.82	48	SO4
3	95	0.52	0.83	19	empty
4	71	0.49	0.84	17	empty
5	103	0.42	0.77	16	empty

Interfaces

5 interfaces between chains.

A–C · 653 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 596 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 477 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 164 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 25 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3QNJ · Crystal structure of the substrate binding domain of E.coli DnaK in complex with the… · the same entry in another collection · chain A against A, TM-score 1.00
P0A6Y8 · AlphaFold monomer V2.0 prediction for chaperone protein dnak (P0A6Y8) · a predicted model of the same protein · chain A against A, TM-score 0.49

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 P0A6Y8
Elsewhere: RCSB PDB 3QNJ · PDBe 3QNJ · UniProt P0A6Y8

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