4R5K: DnaK C-terminus

Name: PDB 4R5K: Crystal structure of the DnaK C-terminus (Dnak-SBD-B)
Published: 2014-09-10
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: chaperone

Crystal structure of the DnaK C-terminus (Dnak-SBD-B). Determined by X-ray diffraction at 1.75 Å resolution. Released 10 Sept 2014.

Method: X-ray diffraction
Resolution: 1.75 Å
Organism: Escherichia coli
Chains: 2
Atoms: 3,930
Mol. weight: 50.47 kDa
Ligands: CA
Released: 10 Sept 2014

Explore 4R5K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4R5K contains 16 α-helices and 24 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: 8 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	387-389	3	1
β-strand	393-394	2	2
β-strand	399-403	5	3
β-strand	407-412	6	3
β-strand	417-418	2	2
β-strand	420-428	9	1
β-strand	436-442	7	3
β-strand	447	1	3
α-helix	448-450	3
β-strand	452-459	8	3
α-helix	462-464	3
β-strand	472-478	7	1
β-strand	484-490	7	1
β-strand	496-501	6	1
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	596-603	8

Chain B: 8 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	387-389	3	1
β-strand	394	1	4
β-strand	399-403	5	5
β-strand	407-412	6	5
β-strand	417	1	4
β-strand	420-428	9	1
β-strand	436-442	7	5
β-strand	447	1	5
α-helix	448-450	3
β-strand	452-459	8	5
α-helix	462-464	3
β-strand	472-478	7	1
β-strand	484-490	7	1
β-strand	496-501	6	1
α-helix	509-521	13
α-helix	523-553	31
α-helix	554-556	3
α-helix	559-576	18
α-helix	581-594	14
α-helix	596-606	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Chaperone protein DnaK	A, B	protein	228	Escherichia coli	P0A6Y8 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4R5K_1 Chaperone protein DnaK (chains A, B)
MHHHHHHIEVLLLDVTPLSLGIETMGGVMTTLIAKNTTIPTKHSQVFSTAEDNQSAVTIH
VLQGERKRAADNKSLGQFNLDGINPAPRGMPQIEVTFDIDADGILHVSAKDKNSGKEQKI
TIKASSGLNEDEIQKMVRDAEANAEADRKFEELVQTRNQGDHLLHSTRKQVEEAGDKLPA
DDKTAIESALTALETALKGEDKAAIEAKMQELAQVSQKLMEIAQQQHA

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1

Water and common crystallization additives (SO4) are not listed.

Primary citation

Structural Basis for the Inhibition of HSP70 and DnaK Chaperones by Small-Molecule Targeting of a C-Terminal Allosteric Pocket. Leu, J.I., Zhang, P., Murphy, M.E. et al. ACS Chem Biol (2014) 9:2508-2516. DOI 10.1021/cb500236y · 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…
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…
7KRU 1.82 Å, Stimulating state of a truncated Hsp70 DnaK fused with a substrate peptide

Browse structure collections

About this viewer

MolViewer shows 4R5K directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.