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Crystal structure of the substrate binding domain of E.COLI dnak in complex with sheep BAC7(1-21)

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: 4JWE
Type: protein
Length: 442 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chaperone protein dnak; Cathelicidin-3
UniProt: P0A6Y8, P50415
Ligands: SO4
Pockets: 5 · best druggability 0.82

Structure

x-ray diffraction · 4 distinct chains · 37% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Chaperone protein dnak	protein	213	41% helix, 28% strand	P0A6Y8
B	Chaperone protein dnak	protein	211	37% helix, 27% strand	P0A6Y8
C	Cathelicidin-3	protein	9	0% helix, 22% strand	P50415
D	Cathelicidin-3	protein	9	0% helix, 22% strand	P50415

Ligands and binding sites

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

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

Pockets

5 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	889	0.82	0.84	87	SO4
2	101	0.52	0.83	19	empty
3	80	0.51	0.84	19	empty
4	146	0.44	0.76	19	empty
5	57	0.27	0.73	11	empty

Interfaces

5 interfaces between chains.

A–D · 734 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 638 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 517 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 130 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 108 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4JWE · Crystal structure of the substrate binding domain of E.coli DnaK in complex with sheep… · the same entry in another collection · chain D against D, 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 0.48
P50415 · AlphaFold monomer V2.0 prediction for cathelicidin-3 (P50415) · a predicted model of the same protein · chain D against A, TM-score 0.46

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
Every structure of UniProt P50415
Elsewhere: RCSB PDB 4JWE · PDBe 4JWE · UniProt P0A6Y8 · UniProt P50415

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