7D3V | pdb_00007d3v

Non-specific and specific interactions work cooperatively to promote cytidine deamination catalyzed by APOBEC3A

PDB DOI: https://doi.org/10.2210/pdb7D3V/pdb
NAKB: 7D3V

Classification: DNA BINDING PROTEIN/DNA
Organism(s): Homo sapiens, synthetic construct
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2020-09-21 Released: 2021-10-06
Deposition Author(s): Cao, C.Y., Liu, Y.P., Lan, W.X.

Experimental Data Snapshot

Method: SOLUTION NMR
Conformers Calculated: 100
Conformers Submitted: 20
Selection Criteria: structures with the lowest energy

wwPDB Validation 3D Report Full Report

Validation slider image for 7D3V

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

Literature

Non-specific and specific interactions work cooperatively to promote cytidine deamination catalyzed by APOBEC3

Liu, Y.P., Lan, W.X., Wang, C.X., Cao, C.Y.

To be published.

Macromolecule Content

Total Structure Weight: 52.25 kDa
Atom Count: 3,652
Modeled Residue Count: 418
Deposited Residue Count: 418
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA dC->dU-editing enzyme APOBEC-3A	A, B	199	Homo sapiens	Mutation(s): 4 Gene Names: APOBEC3A EC: 3.5.4.38
UniProt & NIH Common Fund Data Resources
Find proteins for P31941 (Homo sapiens) Explore P31941 Go to UniProtKB: P31941
PHAROS: P31941 GTEx: ENSG00000128383
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P31941
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism	Image
Entity ID: 2
DNA (5'-D(APTPTPTPTPCPAPAPTPT)-3')	C, D	10	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: SOLUTION NMR
Conformers Calculated: 100
Conformers Submitted: 20
Selection Criteria: structures with the lowest energy

Structure Validation

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Entry History

Deposition Data

Released Date: 2021-10-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-10-06
Type: Initial release
Version 1.1: 2023-06-14
Changes: Other
Version 1.2: 2024-05-15
Changes: Data collection, Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.