MolNFT v1 · #61578 · protein

Crystal structure of the substrate binding domain of E. COLI dnak in complex with a long pyrrhocoricin-derived inhibitor peptide (form B)

3DPQ · Chaperone protein dnak: “Crystal structure of the substrate binding domain of E. COLI dnak in complex with a long…”. X-ray diffraction, 1 ligand (SO4), 14 pockets (best druggability 0.76). MolNFT v1 #61578 on GenesisL1: 3D…

PDB: 3DPQ
Type: protein
Length: 883 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chaperone protein dnak; Inhibitor peptide
UniProt: P0A6Y8
Ligands: SO4
Pockets: 14 · best druggability 0.76

Structure

x-ray diffraction · 6 distinct chains · 33% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Chaperone protein dnak	protein	212	33% helix, 29% strand	P0A6Y8
B	Chaperone protein dnak	protein	212	35% helix, 26% strand	P0A6Y8
E	Chaperone protein dnak	protein	203	33% helix, 29% strand	P0A6Y8
F	Chaperone protein dnak	protein	214	35% helix, 29% strand	P0A6Y8
C, G	Inhibitor peptide	protein	12	0% helix, 17% strand	—
D, H	Inhibitor peptide	protein	9	0% helix, 22% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · chains E, G

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

Pockets

14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	928	0.76	0.79	75	empty
2	723	0.75	0.80	47	empty
3	683	0.75	0.81	50	empty
4	830	0.74	0.79	68	empty
5	114	0.57	0.84	18	empty

Interfaces

11 interfaces between chains.

E–H · 668 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 654 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 652 Å² buried · 8 hydrogen bonds · protein-protein
F–G · 632 Å² buried · 9 hydrogen bonds · protein-protein
E–F · 437 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (nonstandard).

Compared structures

3DPQ · Crystal structure of the substrate binding domain of E. coli DnaK in complex with a long… · 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 E against A, TM-score 0.49

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 3DPQ · PDBe 3DPQ · UniProt P0A6Y8

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