MolNFT v1 · #90973 · protein

Crystal structure of the substrate binding domain of E.COLI dnak in complex with A3-APO(RESIDUES 1 to 20)

4EZP · Chaperone protein dnak: “Crystal structure of the substrate binding domain of E.COLI dnak in complex with A3-APO(RESIDUES 1 to 20)”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.77). MolNFT v1 #90973 on…

PDB: 4EZP
Type: protein
Length: 448 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chaperone protein dnak; Apo-monomer
UniProt: P0A6Y8
Ligands: SO4
Pockets: 5 · best druggability 0.77

Structure

x-ray diffraction · 4 distinct chains · 38% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Chaperone protein dnak	protein	211	38% helix, 28% strand	P0A6Y8
B	Chaperone protein dnak	protein	217	41% helix, 28% strand	P0A6Y8
C	Apo-monomer	protein	7	0% helix, 29% strand	—
D	Apo-monomer	protein	13	0% helix, 15% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 3 copies · chains A, D, B, 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, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	913	0.77	0.80	72	empty
2	550	0.73	0.81	47	SO4
3	90	0.52	0.84	22	empty
4	83	0.50	0.83	19	empty
5	75	0.32	0.74	13	empty

Interfaces

4 interfaces between chains.

A–C · 688 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 636 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 477 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 292 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

4EZP · Crystal structure of the substrate binding domain of E.coli DnaK in complex with… · 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 0.47

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 4EZP · PDBe 4EZP · UniProt P0A6Y8

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