8FAY

Human MUTYH adenine glycosylase bound to DNA containing a transition state analog (1N) paired with d(8-oxo-G)

PDB DOI: https://doi.org/10.2210/pdb8FAY/pdb
NAKB: 8FAY

Classification: HYDROLASE/DNA
Organism(s): Homo sapiens, synthetic construct
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2022-11-29 Released: 2024-05-29
Deposition Author(s): Trasvina-Arenas, C.H., Lin, W.J., Demir, M., Fisher, A.J., David, S.S., Horvath, M.P.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free: 0.209
R-Value Work: 0.180
R-Value Observed: 0.181

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Human MUTYH adenine glycosylase bound to DNA containing a transition state analog (1N) paired with d(8-oxo-G)

Trasvina-Arenas, C.H.

To be published.

Macromolecule Content

Total Structure Weight: 116.54 kDa
Atom Count: 7,492
Modelled Residue Count: 829
Deposited Residue Count: 962
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenine DNA glycosylase	A, D	459	Homo sapiens	Mutation(s): 0 Gene Names: MUTYH, MYH EC: 3.2.2.31
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UIF7 (Homo sapiens) Explore Q9UIF7 Go to UniProtKB: Q9UIF7
PHAROS: Q9UIF7 GTEx: ENSG00000132781
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UIF7
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(APAPGPAPCP(8OG)PTPGPGPAP*C)-3')	B, E	11	synthetic construct
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(PGPTPCPCPAP(NR1)PGPTPCPT)-3')	C, F	11	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SF4 (Subject of Investigation/LOI) Query on SF4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain O [auth D] MOL2 format, chain G [auth A] MOL2 format, chain O [auth D]	G [auth A], O [auth D]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain O [auth D] Interactions & Density Focus chain G [auth A] Focus chain O [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain S [auth D] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain P [auth D] SDF format, chain Q [auth D] SDF format, chain R [auth D] SDF format, chain T [auth D] SDF format, chain U [auth F] MOL2 format, chain S [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] MOL2 format, chain T [auth D] MOL2 format, chain U [auth F]	H [auth A] I [auth A] J [auth A] K [auth A] L [auth A] H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], P [auth D], Q [auth D], R [auth D], S [auth D], T [auth D], U [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth F] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth F]