MolNFT v1 · #61576 · protein

Crystal structure of the substrate binding domain of E. COLI dnak in complex with a short pyrrhocoricin-derived inhibitor peptide

3DPO · Chaperone protein dnak: “Crystal structure of the substrate binding domain of E. COLI dnak in complex with a short…”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.81). MolNFT v1 #61576 on GenesisL1: 3D…

PDB: 3DPO
Type: protein
Length: 446 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chaperone protein dnak; Inhibitor peptide
UniProt: P0A6Y8
Ligands: SO4
Pockets: 5 · best druggability 0.81

Structure

x-ray diffraction · 3 distinct chains · 39% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Chaperone protein dnak	protein	213	40% helix, 27% strand	P0A6Y8
B	Chaperone protein dnak	protein	215	39% helix, 27% strand	P0A6Y8
C, D	Inhibitor peptide	protein	9	0% helix, 22% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 6 copies · chains A, D, B

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	891	0.81	0.84	82	SO4
2	111	0.56	0.84	21	empty
3	78	0.49	0.83	18	empty
4	95	0.39	0.76	17	empty
5	85	0.35	0.75	15	empty

Interfaces

5 interfaces between chains.

A–D · 602 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 600 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 500 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 84 Å² buried · 1 hydrogen bond · protein-protein
B–D · 50 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (nonstandard).

Compared structures

3DPO · Crystal structure of the substrate binding domain of E. coli DnaK in complex with a short… · 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 0.48

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 3DPO · PDBe 3DPO · UniProt P0A6Y8

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