MolNFT v1 · #61577 · protein

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

3DPP · 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), 5 pockets (best druggability 0.81). MolNFT v1 #61577 on GenesisL1: 3D structure…

PDB: 3DPP
Type: protein
Length: 448 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 · 4 distinct chains · 35% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Chaperone protein dnak	protein	212	34% helix, 28% strand	P0A6Y8
B	Chaperone protein dnak	protein	214	40% helix, 28% strand	P0A6Y8
C	Inhibitor peptide	protein	13	0% helix, 15% strand	—
D	Inhibitor peptide	protein	9	0% helix, 33% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	845	0.81	0.84	81	empty
2	131	0.57	0.83	23	empty
3	78	0.48	0.83	17	empty
4	79	0.40	0.78	12	empty
5	101	0.37	0.75	16	empty

Interfaces

5 interfaces between chains.

A–D · 606 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 597 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 491 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 194 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 53 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (nonstandard).

Compared structures

3DPP · Crystal structure of the substrate binding domain of E. coli DnaK in complex with a long… · 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 3DPP · PDBe 3DPP · UniProt P0A6Y8

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