3DPQ: Substrate binding domain of E. coli DnaK

Crystal structure of the substrate binding domain of E. coli DnaK in complex with a long pyrrhocoricin-derived inhibitor peptide (form B). Determined by X-ray diffraction at 2.6 Å resolution. Released 10 Mar 2009.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Escherichia coli
Chains: 8
Atoms: 8,427
Mol. weight: 105.25 kDa
Released: 10 Mar 2009

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

Secondary structure: helices and β-sheets

3DPQ contains 30 α-helices and 52 β-strands across 8 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: 6 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	394-395	2	1
β-strand	399-403	5	2
β-strand	407-412	6	2
β-strand	416-417	2	1
β-strand	420-425	6	3
β-strand	427-428	2	4
β-strand	435-442	8	2
β-strand	447	1	2
α-helix	448-450	3
β-strand	452-460	9	2
β-strand	472-478	7	3
β-strand	484-490	7	3
β-strand	495-501	7	3
α-helix	509-520	12
α-helix	523-548	26
α-helix	562-575	14
α-helix	581-593	13
α-helix	596-598	3

Chain B: 6 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	394	1	5
β-strand	399-403	5	6
β-strand	407-412	6	6
α-helix	416	1
β-strand	417	1	5
β-strand	420-426	7	7
β-strand	427-428	2	8
β-strand	436-437	2	9
β-strand	440-442	3	6
β-strand	447	1	6
α-helix	448-450	3
β-strand	452-455	4	6
β-strand	458-459	2	9
β-strand	472-478	7	7
β-strand	484-490	7	7
β-strand	498-501	4	7
α-helix	509-520	12
α-helix	523-551	29
α-helix	561-575	15
α-helix	581-595	15

Chain C: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	3-4	2	8
α-helix	5-8	4

Chain D: 1 helix, 1 β-strand

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

Chain E: 8 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	394	1	10
β-strand	399-403	5	11
β-strand	407-412	6	11
β-strand	417	1	10
β-strand	420-428	9	12
β-strand	436-442	7	11
β-strand	447	1	11
α-helix	448-450	3
β-strand	452-459	8	11
α-helix	462-464	3
β-strand	472-478	7	12
β-strand	484-490	7	12
β-strand	496-501	6	12
α-helix	509-519	11
α-helix	520-522	3
α-helix	523-546	24
α-helix	561-572	12
α-helix	581-591	11
α-helix	596-598	3

Chain F: 7 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	394-395	2	13
β-strand	399-403	5	14
β-strand	407-412	6	14
β-strand	416-417	2	13
β-strand	420-428	9	15
β-strand	435-442	8	14
β-strand	447	1	14
β-strand	452-460	9	14
α-helix	462-463	2
β-strand	472-478	7	15
β-strand	484-490	7	15
β-strand	496-501	6	15
α-helix	509-521	13
α-helix	523-552	30
α-helix	562-573	12
α-helix	574-576	3
α-helix	581-592	12
α-helix	596-600	5

Chain G: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2-4	3	15
α-helix	5-7	3

Chain H: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2-4	3	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Chaperone protein dnaK	A, B, E, F	protein	219	Escherichia coli	P0A6Y8 (AlphaFold model)
inhibitor peptide	C, D, G, H	protein	20		P37362 (AlphaFold model)

Sequence of entity 1 (A, B, E, F), FASTA

>3DPQ_1 Chaperone protein dnaK (chains A, B, E, F)
VLLLDVTPLSLGIETMGGVMTTLIAKNTTIPTKHSQVFSTAEDNQSAVTIHVLQGERKRA
ADNKSLGQFNLDGINPAPRGMPQIEVTFDIDADGILHVSAKDKNSGKEQKITIKASSGLN
EDEIQKMVRDAEANAEADRKFEELVQTRNQGDHLLHSTRKQVEEAGDKLPADDKTAIESA
LTALETALKGEDKAAIEAKMQELAQVSQKLMEIAQQQHA

Sequence of entity 2 (C, D, G, H), FASTA

>3DPQ_2 inhibitor peptide (chains C, D, G, H)
VDKLYALPRPTPPRPIYNRN

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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