8PFL: WRN helicase domain

Crystal structure of WRN helicase domain in complex with 3. Determined by X-ray diffraction at 1.8 Å resolution. Released 24 Apr 2024.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 1
Atoms: 3,695
Mol. weight: 49.36 kDa
Ligands: ZN, YH8
Released: 24 Apr 2024

Explore 8PFL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8PFL contains 25 α-helices and 16 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: 25 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	524-527	4
α-helix	531-533	3
α-helix	534-544	11
α-helix	551-563	13
β-strand	567-571	5	1
α-helix	578-588	11
β-strand	591-595	5	1
α-helix	599-611	13
β-strand	616-618	3	1
α-helix	625-632	8
β-strand	638-641	4	1
α-helix	643-648	6
α-helix	650-659	10
β-strand	662-667	6	1
α-helix	670-673	4
α-helix	682-685	4
α-helix	686-689	4
α-helix	690-693	4
β-strand	699-703	5	1
α-helix	708-717	10
β-strand	724-728	5	1
β-strand	735-741	7	2
α-helix	746-750	5
α-helix	751-753	3
β-strand	755-757	3	3
β-strand	760-762	3	3
β-strand	767-770	4	2
α-helix	774-785	12
β-strand	791-794	4	2
α-helix	800-811	12
β-strand	817-820	4	2
β-strand	835-839	5	2
α-helix	845-852	8
β-strand	862-868	7	2
α-helix	870-880	11
α-helix	886-904	19
α-helix	909-917	9
α-helix	920-925	6
α-helix	926-928	3
β-strand	936	1	2
α-helix	937-943	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Bifunctional 3'-5' exonuclease/ATP-dependent helicase WRN	A	protein	431	Homo sapiens	Q14191 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8PFL_1 Bifunctional 3'-5' exonuclease/ATP-dependent helicase WRN (chains A)
GPNEGEEDDDKDFLWPAPNEEQVTCLKMYFGHSSFKPVQWKVIHSVLEEARDNVAVMATG
YGKSLCFQYPPVYVGKIGLVISPLISLMEDQVLQLKMSNIPACFLGSAQSANVLTDIKLG
KYRIVYVTPEYCSGNMGLLQQLEADIGITLIAVDEAHCISEWGHDFRDSFRKLGSLKTAL
PMVPIVALTATASSSIREDIVRCLNLRNPQITCTGFDRPNLYLEVRRKTGNILQDLQPFL
VKTSSHWEFEGPTIIYCPSRKMTQQVTGELAKLNLSCGTYHAGMSFSTAKDIHHRFVRDE
IQCVIATIAFGMGINKADIRQVIHYGAPKDMESYYQEIGRAGRDGLQSSCHVLWAPADIN
LNRHLLTEIRNAKFRLYKLKMMAKMEKYLHSSRCRRQIILSHFEDKQVQKASLGIMGTEK
CCDNCRSALDH

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
YH8	2-[2-(3,6-dihydro-2~{H}-pyran-4-yl)-5-ethyl-7-oxidanylidene-6-[4-(3-oxidanylpyr…	C32 H33 F3 N8 O5	1

Primary citation

Discovery of WRN inhibitor HRO761 with synthetic lethality in MSI cancers. Ferretti, S., Hamon, J., de Kanter, R. et al. Nature (2024) 629:443-449. DOI 10.1038/s41586-024-07350-y · PubMed

Other PDB entries of the same protein (UniProt Q14191 (AlphaFold model), which also has an AlphaFold model), best resolution first:

10AK 1.37 Å, Crystal Structure of Human WRN helicase with compound 4
7GQU 1.54 Å, Crystal Structure of Werner helicase fragment 517-945 in covalent complex with…
9OWB 1.56 Å, Human WRN helicase in complex with allosteric ligand Compound 6
7GQS 1.57 Å, Crystal Structure of Werner helicase fragment 517-945 in complex with ADP
9MJU 1.58 Å, Crystal structure of WRN helicase with allosteric fragment 1
7XUT 1.6 Å, Crystal structure of RPA70N-WRN fusion
8PFP 1.6 Å, Crystal structure of WRN helicase domain in complex with ATPgammaS
9MJY 1.63 Å, Crystal structure of WRN helicase with bound allosteric compound 1
9OG8 1.66 Å, Crystal structure of WRN in complex with compound 43
9OWC 1.67 Å, Human WRN helicase in complex with allosteric ligand Compound 7
9MJZ 1.7 Å, Crystal structure of WRN helicase with bound allosteric compound 3
9MJT 1.73 Å, Crystal structure of apo WRN helicase in Form D

Browse structure collections

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