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

Extended structure of citidine deaminase domain of APOBEC3G. Determined by solution NMR. Released 2 Jun 2009.

Method: Solution NMR
Organism: Homo sapiens
Chains: 1
Atoms: 1,605
Mol. weight: 23.58 kDa
Ligands: ZN
Released: 2 Jun 2009

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

Secondary structure: helices and β-sheets

2KEM contains 8 α-helices and 11 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, 11 β-strands

Element	Residues	Length	Sheet
α-helix	12-16	5
β-strand	31	1	1
β-strand	34-37	4	2
α-helix	68-79	12
β-strand	81	1	3
β-strand	85	1	3
β-strand	86-89	4	2
β-strand	92-93	2	1
α-helix	99-105	7
α-helix	106-110	5
β-strand	116-117	2	2
β-strand	118	1	4
β-strand	120-121	2	1
α-helix	132-137	6
α-helix	138-142	5
β-strand	144	1	4
β-strand	147	1	1
α-helix	150-160	11
α-helix	173-189	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA dC->dU-editing enzyme APOBEC-3G	A	protein	202	Homo sapiens	Q9HC16 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2KEM_1 DNA dC->dU-editing enzyme APOBEC-3G (chains A)
GPLGSPGFEILRHSMDPPTFTFNFNNEPWVRGRHETYLCYEVERMHNDTWVKLNQRRGFL
ANQAPHKHGFLEGRHAELCFLDVIPFWKLDLDQDYRVTCFTSWSPCFSCAQEMAKFISKN
KHVSLCIKTARIYDDQGRAQEGLRTLAEAGAKISIMTYSEFKHCWDTFVDHQGAPFQPWD
GLDEHSQDLSGRLRAILQNQEN

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Primary citation

An extended structure of the APOBEC3G catalytic domain suggests a unique holoenzyme model. Harjes, E., Gross, P.J., Chen, K.M. et al. J Mol Biol (2009) 389:819-832. DOI 10.1016/j.jmb.2009.04.031 · 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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