7R6V | pdb_00007r6v

Human EXOG complexed with dRP-containing DNA

PDB DOI: https://doi.org/10.2210/pdb7R6V/pdb
NAKB: 7R6V

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

Deposited: 2021-06-23 Released: 2022-08-24
Deposition Author(s): Szymanski, M.R., Yin, Y.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free:
0.240 (Depositor), 0.244 (DCC)
R-Value Work:
0.200 (Depositor), 0.213 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Human EXOG possesses strong AP hydrolysis activity

Szymanski, M.R., Yin, Y.W.

To be published.

Macromolecule Content

Total Structure Weight: 169.35 kDa
Atom Count: 11,230
Modeled Residue Count: 1,237
Deposited Residue Count: 1,332
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclease EXOG, mitochondrial	A [auth D], B [auth E], G, H [auth I]	311	Homo sapiens	Mutation(s): 0 Gene Names: EXOG, ENDOGL1, ENDOGL2, ENGL EC: 3.1.30
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2C4 (Homo sapiens) Explore Q9Y2C4 Go to UniProtKB: Q9Y2C4
PHAROS: Q9Y2C4 GTEx: ENSG00000157036
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y2C4
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 2
DNA (5'-D(CPTPGPAPCPGPTPGPCPG)-3')	C [auth F], D [auth H], I [auth J], J [auth K]	10	synthetic construct
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 3
DNA (5'-D(CPGPCPAPCPGPTPCPAPGPAPA)-3')	E [auth B], F [auth A], K [auth L], L [auth M]	12	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

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