7N6M: Substrate-binding domain of E. coli DnaK

Crystal structure of the substrate-binding domain of E. coli DnaK in complex with the peptide RQKPLLGLSR. Determined by X-ray diffraction at 1.82 Å resolution. Released 23 Jun 2021.

Method: X-ray diffraction
Resolution: 1.82 Å
Organism: Escherichia coli (strain K12)
Chains: 2
Atoms: 1,685
Mol. weight: 25.09 kDa
Released: 23 Jun 2021

Explore 7N6M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7N6M contains 10 α-helices and 13 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 10 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	394	1	1
β-strand	399-403	5	2
β-strand	407-412	6	2
α-helix	416	1
β-strand	417	1	1
β-strand	420-426	7	3
β-strand	427-428	2	4
β-strand	436-442	7	2
β-strand	447	1	2
α-helix	448-450	3
β-strand	452-459	8	2
α-helix	462-463	2
β-strand	472-478	7	3
α-helix	483	1
β-strand	484-490	7	3
β-strand	496-501	6	3
α-helix	509-521	13
α-helix	523-553	31
α-helix	554-556	3
α-helix	559-577	19
α-helix	581-594	14
α-helix	596-602	7

Chain B: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	256-257	2	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Chaperone protein DnaK	A	protein	219	Escherichia coli (strain K12)	P0A6Y8 (AlphaFold model)
Alkaline phosphatase peptide	B	protein	10	Escherichia coli (strain K12)	P00634 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7N6M_1 Chaperone protein DnaK (chains A)
VLLLDVTPLSLGIETMGGVMTTLIAKNTTIPTKHSQVFSTAEDNQSAVTIHVLQGERKRA
ADNKSLGQFNLDGINPAPRGMPQIEVTFDIDADGILHVSAKDKNSGKEQKITIKASSGLN
EDEIQKMVRDAEANAEADRKFEELVQTRNQGDHLLHSTRKQVEEAGDKLPADDKTAIESA
LTALETALKGEDKAAIEAKMQELAQVSQKLMEIAQQQHA

Sequence of entity 2 (B), FASTA

>7N6M_2 Alkaline phosphatase peptide (chains B)
RQKPLLGLSR

Primary citation

Selective promiscuity in the binding of E. coli Hsp70 to an unfolded protein. Clerico, E.M., Pozhidaeva, A.K., Jansen, R.M. et al. Proc Natl Acad Sci U S A (2021) 118. DOI 10.1073/pnas.2016962118 · PubMed

Other PDB entries of the same protein (UniProt P0A6Y8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4F01 1.4 Å, Crystal structure of an artificial dimeric DnaK complex
7RAX 1.41 Å, ATP-binding state of the nucleotide-binding domain of Hsp70 DnaK mutant T199A
13JG 1.52 Å, E. coli DnaK bound to peptide PA1, structure B
4HY9 1.55 Å, Crystal structure of the substrate binding domain of E.coli DnaK in complex with…
4JNF 1.62 Å, Allosteric opening of the polypeptide-binding site when an Hsp70 binds ATP
4EZP 1.65 Å, Crystal structure of the substrate binding domain of E.coli DnaK in complex with…
4EZX 1.7 Å, Crystal structure of the substrate binding domain of E.coli DnaK in complex with the…
4HYB 1.7 Å, Crystal structure of the substrate binding domain of E.coli DnaK in complex with…
4R5K 1.75 Å, Crystal structure of the DnaK C-terminus (Dnak-SBD-B)
4EZN 1.8 Å, Crystal structure of the substrate binding domain of E.coli DnaK in complex with…
4EZW 1.8 Å, Crystal structure of the substrate binding domain of E.coli DnaK in complex with the…
4JWC 1.8 Å, Crystal structure of the substrate binding domain of E.coli DnaK in complex with bovine…

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