4JWD: Substrate binding domain of E.coli DnaK

Crystal structure of the substrate binding domain of E.coli DnaK in complex with bovine Bac7(15-28). Determined by X-ray diffraction at 1.95 Å resolution. Released 13 Nov 2013.

Method: X-ray diffraction
Resolution: 1.95 Å
Organisms: Escherichia coli, Bos taurus
Chains: 4
Atoms: 3,672
Mol. weight: 51.13 kDa
Released: 13 Nov 2013

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

Secondary structure: helices and β-sheets

4JWD contains 16 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: 7 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	436-442	7	2
β-strand	447	1	2
α-helix	448-450	3
β-strand	452-459	8	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

Chain B: 9 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	554-556	3
α-helix	559-577	19
α-helix	581-594	14
α-helix	596-601	6

Chain C: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	17-18	2	7

Chain D: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	16-18	3	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Chaperone protein DnaK	A, B	protein	219	Escherichia coli	P0A6Y8 (AlphaFold model)
Cathelicidin-3	C, D	protein	14	Bos taurus	P19661 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4JWD_1 Chaperone protein DnaK (chains A, B)
VLLLDVTPLSLGIETMGGVMTTLIAKNTTIPTKHSQVFSTAEDNQSAVTIHVLQGERKRA
ADNKSLGQFNLDGINPAPRGMPQIEVTFDIDADGILHVSAKDKNSGKEQKITIKASSGLN
EDEIQKMVRDAEANAEADRKFEELVQTRNQGDHLLHSTRKQVEEAGDKLPADDKTAIESA
LTALETALKGEDKAAIEAKMQELAQVSQKLMEIAQQQHA

Sequence of entity 2 (C, D), FASTA

>4JWD_2 Cathelicidin-3 (chains C, D)
PRPLPFPRPGPRPI

Primary citation

Structural Identification of DnaK Binding Sites within Bovine and Sheep Bactenecin Bac7. Zahn, M., Kieslich, B., Berthold, N. et al. Protein Pept Lett (2014) 21:407-412. 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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