5MKR: HSP72-NBD

HSP72-NBD bound to compound TCI 8 - Tyr15 in up-conformation. Determined by X-ray diffraction at 1.87 Å resolution. Released 1 Mar 2017.

Method: X-ray diffraction
Resolution: 1.87 Å
Organism: Homo sapiens
Chains: 1
Atoms: 3,843
Mol. weight: 43.87 kDa
Ligands: TI8, FLC
Released: 1 Mar 2017

Explore 5MKR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5MKR contains 19 α-helices and 19 β-strands across 1 chain. 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: 19 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	2-6	5
β-strand	7-11	5	1
β-strand	15-22	8	1
β-strand	25-28	4	1
α-helix	29-30	2
β-strand	38-39	2	1
β-strand	42-44	3	2
β-strand	49-51	3	2
α-helix	53-57	5
α-helix	59-61	3
α-helix	63-65	3
β-strand	66-67	2	2
α-helix	70-73	4
α-helix	81-87	7
β-strand	93-97	5	3
β-strand	100-107	8	3
β-strand	110-114	5	3
α-helix	116-135	20
β-strand	141-146	6	1
α-helix	152-164	13
β-strand	168-174	7	1
α-helix	175-182	8
β-strand	192-200	9	4
β-strand	205-213	9	4
β-strand	216-225	10	4
α-helix	230-249	20
α-helix	257-273	17
β-strand	279-288	10	5
β-strand	291-298	8	5
α-helix	299-305	7
α-helix	307-311	5
α-helix	314-323	10
α-helix	328-330	3
β-strand	333-337	5	4
α-helix	339-342	4
α-helix	344-353	10
β-strand	360	1	4
α-helix	368-384	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Heat shock 70 kDa protein 1A	A	protein	394	Homo sapiens	P0DMV8 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5MKR_1 Heat shock 70 kDa protein 1A (chains A)
GPLGSMAKAAAIGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAA
KNQVALNPQNTVFDAKRLIGRKFGDPVVQSDMKHWPFQVINDGDKPKVQVSYKGETKAFY
PEEISSMVLTKMKEIAEAYLGYPVTNAVITVPAYFNDSQRQATKDAGVIAGLNVLRIINE
PTAAAIAYGLDRTGKGERNVLIFDLGGGTFDVSILTIDDGIFEVKATAGDTHLGGEDFDN
RLVNHFVEEFKRKHKKDISQNKRAVRRLRTACERAKRTLSSSTQASLEIDSLFEGIDFYT
SITRARFEELCSDLFRSTLEPVEKALRDAKLDKAQIHDLVLVGGSTRIPKVQKLLQDFFN
GRDLNKSINPDEAVAYGAAVQAAILIKSTRAAAS

Ligands and cofactors

ID	Name	Formula	Copies
TI8	3-[(2~{R},3~{S},4~{R},5~{R})-5-[6-azanyl-8-[(4-chlorophenyl)methylamino]purin-9…	C22 H25 Cl N6 O5	1
FLC	Citrate anion	C6 H5 O7	1

Primary citation

An Irreversible Inhibitor of HSP72 that Unexpectedly Targets Lysine-56. Pettinger, J., Le Bihan, Y.V., Widya, M. et al. Angew Chem Int Ed Engl (2017) 56:3536-3540. DOI 10.1002/anie.201611907 · PubMed

Other PDB entries of the same protein (UniProt P0DMV8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5BN8 1.34 Å, Crystal structure of nucleotide-free human Hsp70 NBD.
6K39 1.4 Å, Structural analysis of AIMP2-DX2 and HSP70 interaction
6G3R 1.4 Å, Structure of tellurium-centred Anderson-Evans polyoxotungstate (TEW) bound to the…
6ZYI 1.52 Å, Crystal structure of HSP70 ATPase domain in complex with ADP and calcium
5AQW 1.53 Å, Fragment-based screening of HSP70 sheds light on the functional role of ATP-binding site…
3Q49 1.54 Å, Crystal structure of the TPR domain of CHIP complexed with Hsp70-C peptide
5AQY 1.56 Å, Fragment-based screening of HSP70 sheds light on the functional role of ATP-binding site…
3ATV 1.58 Å, Crystal structure of human Hsp70 NBD in the ADP-bound and Mg ion-free state
3ATU 1.65 Å, Crystal structure of human Hsp70 NBD in the ADP- and Mg ion-bound state
5AQZ 1.65 Å, HSP72 with adenosine-derived inhibitor
6FHK 1.66 Å, Structure of a modified protein containing a genetically encoded phosphoserine
5BN9 1.69 Å, Crystal structure of ADP bound human Hsp70 NBD mutant R272K.

Browse structure collections

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