MolNFT v1 · #90980 · protein

Crystal structure of the substrate binding domain of E.COLI dnak in complex with the designer peptide nrllltg

4EZW · Chaperone protein dnak: “Crystal structure of the substrate binding domain of E.COLI dnak in complex with the designer peptide nrllltg”. X-ray diffraction, 1 ligand (SO4), 9 pockets (best druggability 0.84). MolNFT v1 #90980 on…

PDB: 4EZW
Type: protein
Length: 888 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chaperone protein dnak; Synthetic peptide nrllltg
UniProt: P0A6Y8
Ligands: SO4
Pockets: 9 · best druggability 0.84

Structure

x-ray diffraction · 4 distinct chains · 40% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Chaperone protein dnak	protein	214	39% helix, 30% strand	P0A6Y8
B, C	Chaperone protein dnak	protein	215	41% helix, 30% strand	P0A6Y8
D	Chaperone protein dnak	protein	216	42% helix, 29% strand	P0A6Y8
E, F, G, H	Synthetic peptide nrllltg	protein	7	0% helix, 29% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 9 copies · chains A, C, B, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1045	0.84	0.85	79	SO4
2	114	0.42	0.76	14	empty
3	106	0.41	0.77	15	empty
4	97	0.40	0.77	15	empty
5	93	0.40	0.77	17	empty

Interfaces

7 interfaces between chains.

A–C · 988 Å² buried · 19 hydrogen bonds · protein-protein
B–D · 984 Å² buried · 19 hydrogen bonds · protein-protein
C–G · 580 Å² buried · 7 hydrogen bonds · protein-protein
D–H · 579 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 553 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

4EZW · Crystal structure of the substrate binding domain of E.coli DnaK in complex with the… · the same entry in another collection · chain H against H, TM-score 1.00
P0A6Y8 · AlphaFold monomer V2.0 prediction for chaperone protein dnak (P0A6Y8) · a predicted model of the same protein · chain C 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
Elsewhere: RCSB PDB 4EZW · PDBe 4EZW · UniProt P0A6Y8

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