MolNFT v1 · #90971 · protein

Crystal structure of the substrate binding domain of E.COLI dnak in complex with pyrrhocoricin

4EZN · Chaperone protein dnak: “Crystal structure of the substrate binding domain of E.COLI dnak in complex with pyrrhocoricin”. X-ray diffraction, 5 pockets (best druggability 0.77). MolNFT v1 #90971 on GenesisL1: 3D structure, binding…

PDB: 4EZN
Type: protein
Length: 441 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chaperone protein dnak; Pyrrhocoricin
UniProt: P0A6Y8, P37362
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	37% helix, 28% strand	P0A6Y8
B	Chaperone protein dnak	protein	215	42% helix, 28% strand	P0A6Y8
C	Pyrrhocoricin	protein	6	0% helix, 17% strand	P37362
D	Pyrrhocoricin	protein	9	0% helix, 22% strand	P37362

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	744	0.77	0.81	65	empty
2	506	0.76	0.84	45	empty
3	74	0.50	0.84	18	empty
4	98	0.48	0.81	20	empty
5	60	0.32	0.76	12	empty

Interfaces

5 interfaces between chains.

A–C · 555 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 514 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 456 Å² buried · 9 hydrogen bonds · protein-protein
A–D · 130 Å² buried · 1 hydrogen bond · protein-protein
B–C · 24 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4EZN · Crystal structure of the substrate binding domain of E.coli DnaK in complex with… · the same entry in another collection · chain D against D, TM-score 1.00
P37362 · AlphaFold monomer V2.0 prediction for pyrrhocoricin (P37362) · a predicted model of the same protein · chain C against A, TM-score 0.68
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 P37362
Elsewhere: RCSB PDB 4EZN · PDBe 4EZN · UniProt P0A6Y8 · UniProt P37362

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