3DPO: Substrate binding domain of E. coli DnaK

Crystal structure of the substrate binding domain of E. coli DnaK in complex with a short pyrrhocoricin-derived inhibitor peptide. Determined by X-ray diffraction at 2.1 Å resolution. Released 10 Mar 2009.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Escherichia coli
Chains: 4
Atoms: 4,033
Mol. weight: 50.93 kDa
Released: 10 Mar 2009

Explore 3DPO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3DPO contains 18 α-helices and 25 β-strands across 4 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, 11 β-strands

Element	Residues	Length	Sheet
β-strand	394	1	1
β-strand	399-403	5	2
β-strand	407-412	6	2
β-strand	417	1	1
β-strand	420-428	9	3
β-strand	435-442	8	2
β-strand	447	1	2
α-helix	448-450	3
β-strand	452-460	9	2
α-helix	462-464	3
β-strand	472-478	7	3
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	559-576	18
α-helix	581-593	13
α-helix	596-600	5

Chain B: 8 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	394	1	4
β-strand	399-403	5	5
β-strand	407-412	6	5
α-helix	416	1
β-strand	417	1	4
β-strand	420-426	7	6
β-strand	427-428	2	7
β-strand	436-442	7	5
β-strand	447	1	5
α-helix	448-450	3
β-strand	452-459	8	5
α-helix	462-463	2
β-strand	472-478	7	6
β-strand	484-490	7	6
β-strand	496-501	6	6
α-helix	509-521	13
α-helix	523-553	31
α-helix	559-575	17
α-helix	581-593	13
α-helix	596-602	7

Chain C: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	3-4	2	7
α-helix	5-7	3

Chain D: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2-4	3	3
α-helix	5-7	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Chaperone protein dnaK	A, B	protein	219	Escherichia coli	P0A6Y8 (AlphaFold model)
inhibitor peptide	C, D	protein	11		P37362 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3DPO_1 Chaperone protein dnaK (chains A, B)
VLLLDVTPLSLGIETMGGVMTTLIAKNTTIPTKHSQVFSTAEDNQSAVTIHVLQGERKRA
ADNKSLGQFNLDGINPAPRGMPQIEVTFDIDADGILHVSAKDKNSGKEQKITIKASSGLN
EDEIQKMVRDAEANAEADRKFEELVQTRNQGDHLLHSTRKQVEEAGDKLPADDKTAIESA
LTALETALKGEDKAAIEAKMQELAQVSQKLMEIAQQQHA

Sequence of entity 2 (C, D), FASTA

>3DPO_2 inhibitor peptide (chains C, D)
VDKLYALPRPT

Primary citation

Allosteric coupling between the lid and interdomain linker in DnaK revealed by inhibitor binding studies. Liebscher, M., Roujeinikova, A. J Bacteriol (2009) 191:1456-1462. DOI 10.1128/JB.01131-08 · 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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