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

Analyse Crystal structure of the substrate binding domain of E.COLI dnak in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

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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