6VNP | pdb_00006vnp

Crystal structure of DPO4 extension past 8-oxoadenine (oxoA) and dT

PDB DOI: https://doi.org/10.2210/pdb6VNP/pdb
NAKB: 6VNP

Classification: TRANSFERASE/DNA
Organism(s): Homo sapiens, Saccharolobus solfataricus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-01-29 Released: 2021-02-03
Deposition Author(s): Jung, H., Lee, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free:
0.242 (Depositor), 0.242 (DCC)
R-Value Work:
0.199 (Depositor), 0.202 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of DPO4 extension past 8-oxoadenine (oxoA) and dT

Jung, H., Lee, S.

To be published.

Macromolecule Content

Total Structure Weight: 198.6 kDa
Atom Count: 14,020
Modeled Residue Count: 1,489
Deposited Residue Count: 1,496
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase IV	C [auth A], F [auth D], I [auth G], L [auth J]	341	Saccharolobus solfataricus	Mutation(s): 0 Gene Names: dbh, SSOP1_2570, SULA_0242, SULB_0243, SULC_0242, SULG_01230, SULH_01230, SULI_01230, SULM_01230, SULN_01230... dbh, SSOP1_2570, SULA_0242, SULB_0243, SULC_0242, SULG_01230, SULH_01230, SULI_01230, SULM_01230, SULN_01230, SULO_01240, SULZ_01250 EC: 2.7.7.7
UniProt
Find proteins for Q97W02 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore Q97W02 Go to UniProtKB: Q97W02
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q97W02
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 1
DNA (5'-D(PGPGPGPGPGPAPAPGPGPAPTPTPCPT)-3')	A [auth P], D [auth B], G [auth E], J [auth H]	14	Homo sapiens
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 2
DNA (5'-D(TPTPCPAPT(R5M)PGPAPAPTPCPCPTPTPCPCPCPCP*C)-3')	B [auth T], E [auth C], H [auth F], K [auth I]	19	Homo sapiens
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DZ4 (Subject of Investigation/LOI) Query on DZ4 Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain P [auth D] SDF format, chain S [auth G] SDF format, chain V [auth J] MOL2 format, chain M [auth A] MOL2 format, chain P [auth D] MOL2 format, chain S [auth G] MOL2 format, chain V [auth J] mmCIF format, chain M [auth A] mmCIF format, chain P [auth D] mmCIF format, chain S [auth G] mmCIF format, chain V [auth J]	M [auth A], P [auth D], S [auth G], V [auth J]	2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine C₁₀ H₁₇ N₆ O₁₁ P₃ WKIPJDSLGCBQCU-RRKCRQDMSA-N		Interactions Focus chain M [auth A] Focus chain P [auth D] Focus chain S [auth G] Focus chain V [auth J] Interactions & Density Focus chain M [auth A] Focus chain P [auth D] Focus chain S [auth G] Focus chain V [auth J]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain X [auth J] SDF format, chain W [auth J] SDF format, chain U [auth G] SDF format, chain T [auth G] SDF format, chain R [auth D] SDF format, chain Q [auth D] SDF format, chain O [auth A] SDF format, chain N [auth A] MOL2 format, chain X [auth J] MOL2 format, chain W [auth J] MOL2 format, chain U [auth G] MOL2 format, chain T [auth G] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] mmCIF format, chain X [auth J] mmCIF format, chain W [auth J] mmCIF format, chain U [auth G] mmCIF format, chain T [auth G] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A]	N [auth A] O [auth A] Q [auth D] R [auth D] T [auth G] N [auth A], O [auth A], Q [auth D], R [auth D], T [auth G], U [auth G], W [auth J], X [auth J]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain O [auth A] Focus chain Q [auth D] Focus chain R [auth D] Focus chain T [auth G] Focus chain U [auth G] Focus chain W [auth J] Focus chain X [auth J] Interactions & Density Focus chain N [auth A] Focus chain O [auth A] Focus chain Q [auth D] Focus chain R [auth D] Focus chain T [auth G] Focus chain U [auth G] Focus chain W [auth J] Focus chain X [auth J]