3V4K: DNA dC->dU-editing enzyme APOBEC-3G

First-In-Class Small Molecule Inhibitors of the Single-strand DNA Cytosine Deaminase APOBEC3G. Determined by X-ray diffraction at 1.38 Å resolution. Released 25 Jan 2012.

Method: X-ray diffraction
Resolution: 1.38 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,539
Mol. weight: 47.65 kDa
Ligands: ZN, MG
Released: 25 Jan 2012

Explore 3V4K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3V4K contains 27 α-helices and 16 β-strands across 2 chains. 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: 15 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	196	1
β-strand	197	1	1
α-helix	198	1
α-helix	199-206	8
β-strand	219-228	10	2
β-strand	231-234	4	2
α-helix	236-238	3
β-strand	240-243	4	2
α-helix	244-248	5
α-helix	254-257	4
α-helix	258-265	8
α-helix	266-269	4
β-strand	277-283	7	2
α-helix	286-288	3
α-helix	289-301	13
β-strand	305-311	7	2
α-helix	321-330	10
β-strand	334-337	4	2
α-helix	340-350	11
β-strand	351	1	1
α-helix	356-358	3
α-helix	360-361	2
α-helix	364-379	16

Chain B: 12 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	197	1	3
α-helix	199-206	8
β-strand	219-228	10	4
β-strand	231-234	4	4
β-strand	240-243	4	4
α-helix	244-248	5
α-helix	254-257	4
α-helix	258-265	8
α-helix	266-269	4
β-strand	277-285	9	4
α-helix	286-288	3
α-helix	289-301	13
β-strand	305-313	9	4
α-helix	321-330	10
β-strand	334-337	4	4
α-helix	340-350	11
β-strand	351	1	3
α-helix	356-358	3
α-helix	360-361	2
α-helix	364-379	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA dC->dU-editing enzyme APOBEC-3G	A, B	protein	203	Homo sapiens	Q9HC16 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3V4K_1 DNA dC->dU-editing enzyme APOBEC-3G (chains A, B)
GPLGSPEFELGTTEILRHSMDPPTFTFNFNNEPWVRGRHETYLCYEVERMHNDTWVKLNQ
RRGFLANQAPHKHGFLEGRHAELCFLDVIPFWKLDLDQDYRVTCFTSWSPCFSCAQEMAK
FISKNKHVSLCIKTARIYDDQGRCQEGLRTLAEAGAKISIMTYSEFKHCWDTFVDHQGAP
FQPWDGLDEHSQDLSGRLRAILQ

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4
MG	Magnesium ion	Mg	2

Water and common crystallization additives (CL) are not listed.

Primary citation

First-In-Class Small Molecule Inhibitors of the Single-Strand DNA Cytosine Deaminase APOBEC3G. Li, M., Shandilya, S.M., Carpenter, M.A. et al. ACS Chem Biol (2012) 7:506-517. DOI 10.1021/cb200440y · PubMed

Other PDB entries of the same protein (UniProt Q9HC16 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7UXD 1.5 Å, Crystal structure of APOBEC3G Catalytic domain complex with ssDNA containing 2'-deoxy…
4ROW 1.7 Å, The crystal structure of novel APOBEC3G CD2 head-to-tail dimer suggests the binding mode…
4ROV 1.8 Å, The crystal structure of novel APOBEC3G CD2 head-to-tail dimer suggests the binding mode…
6BUX 1.86 Å, Crystal structure of APOBEC3G catalytic domain complex with substrate ssDNA
5ZVB 2.0 Å, APOBEC3F Chimeric Catalytic Domain in Complex with DNA(dT9)
3V4J 2.04 Å, First-In-Class Small Molecule Inhibitors of the Single-strand DNA Cytosine Deaminase…
3IR2 2.25 Å, Crystal structure of the APOBEC3G catalytic domain
3E1U 2.3 Å, The Crystal Structure of the Anti-Viral APOBEC3G Catalytic Domain
3IQS 2.3 Å, Crystal structure of the anti-viral APOBEC3G catalytic domain
5ZVA 2.3 Å, APOBEC3F Chimeric Catalytic Domain in Complex with DNA(dC9)
8J62 2.5 Å, Cryo-EM structure of APOBEC3G-Vif complex
8CX0 2.7 Å, Cryo-EM structure of human APOBEC3G/HIV-1 Vif/CBFbeta/ELOB/ELOC monomeric complex

Browse structure collections

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