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Crystal structure of the substrate binding domain of E.COLI dnak in complex with bovine BAC7(15-28)

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: 4JWD
Type: protein
Length: 439 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chaperone protein dnak; Cathelicidin-3
UniProt: P0A6Y8, P19661
Ligands: SO4
Pockets: 6 · best druggability 0.75

Structure

x-ray diffraction · 3 distinct chains · 39% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Chaperone protein dnak	protein	211	38% helix, 27% strand	P0A6Y8
B	Chaperone protein dnak	protein	214	42% helix, 27% strand	P0A6Y8
C, D	Cathelicidin-3	protein	7	0% helix, 29% strand	P19661

Ligands and binding sites

SO4 · Sulfate ion · ion · 3 copies · chains A, B

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	546	0.75	0.83	47	empty
2	590	0.74	0.81	58	SO4
3	84	0.51	0.84	18	empty
4	93	0.49	0.82	19	empty
5	67	0.35	0.77	14	empty

Interfaces

3 interfaces between chains.

B–C · 599 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 589 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 492 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

4JWD · Crystal structure of the substrate binding domain of E.coli DnaK in complex with bovine… · the same entry in another collection · chain D against D, TM-score 1.00
P19661 · AlphaFold monomer V2.0 prediction for cathelicidin-3 (P19661) · a predicted model of the same protein · chain C against A, TM-score 0.48
P0A6Y8 · AlphaFold monomer V2.0 prediction for chaperone protein dnak (P0A6Y8) · a predicted model of the same protein · chain A against A, TM-score 0.47

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 P19661
Elsewhere: RCSB PDB 4JWD · PDBe 4JWD · UniProt P0A6Y8 · UniProt P19661

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