MolNFT v1 · #90981 · protein

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

4EZX · Chaperone protein dnak: “Crystal structure of the substrate binding domain of E.COLI dnak in complex with the designer peptide nrlmltg”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.51). MolNFT v1 #90981 on…

PDB: 4EZX
Type: protein
Length: 437 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chaperone protein dnak; Synthetic peptide nrlmltg
UniProt: P0A6Y8
Ligands: SO4
Pockets: 5 · best druggability 0.51

Structure

x-ray diffraction · 3 distinct chains · 38% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Chaperone protein dnak	protein	212	38% helix, 27% strand	P0A6Y8
B	Chaperone protein dnak	protein	211	39% helix, 27% strand	P0A6Y8
C, D	Synthetic peptide nrlmltg	protein	7	0% helix, 29% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 5 copies · chains A, C

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

Pockets

5 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	93	0.51	0.83	19	empty
2	249	0.49	0.74	30	empty
3	70	0.48	0.84	18	empty
4	81	0.37	0.76	16	empty
5	71	0.35	0.76	16	empty

Interfaces

3 interfaces between chains.

B–D · 584 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 580 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 438 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

4EZX · 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 B against A, TM-score 0.48

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 4EZX · PDBe 4EZX · UniProt P0A6Y8

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