2KBO: DNA dC->dU-editing enzyme APOBEC-3G

Structure, interaction, and real-time monitoring of the enzymatic reaction of wild type APOBEC3G. Determined by solution NMR. Released 3 Feb 2009.

Method: Solution NMR
Organism: Homo sapiens
Chains: 1
Atoms: 1,611
Mol. weight: 22.99 kDa
Ligands: ZN
Released: 3 Feb 2009

Explore 2KBO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2KBO contains 8 α-helices and 5 β-strands across 1 chain. 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: 8 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	9-14	6
β-strand	31-38	8	1
β-strand	41-42	2	1
α-helix	68-79	12
β-strand	86-92	7	1
α-helix	99-106	8
α-helix	107-111	5
β-strand	115-121	7	1
α-helix	130-132	3
α-helix	133-141	9
β-strand	143-147	5	1
α-helix	150-160	11
α-helix	174-189	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA dC->dU-editing enzyme APOBEC-3G	A	protein	194	Homo sapiens	Q9HC16 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2KBO_1 DNA dC->dU-editing enzyme APOBEC-3G (chains A)
HMLRHSMDPPTFTFNFNNEPWVRGRHETYLCYEVERMHNDTWVLLNQRRGFLCNQAPHKH
GFLEGRHAELCFLDVIPFWKLDLDQDYRVTCFTSWSPCFSCAQEMAKFISKNKHVSLCIF
TARIYDDQGRCQEGLRTLAEAGAKISIMTYSEFKHCWDTFVDHQGCPFQPWDGLDEHSQD
LSGRLRAILQNQEN

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Primary citation

Structure, interaction and real-time monitoring of the enzymatic reaction of wild-type APOBEC3G. Furukawa, A., Nagata, T., Matsugami, A. et al. EMBO J (2009) 28:440-451. DOI 10.1038/emboj.2008.290 · PubMed

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

3V4K 1.38 Å, First-In-Class Small Molecule Inhibitors of the Single-strand DNA Cytosine Deaminase…
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

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