6BUX: PDB entry 6BUX

Crystal structure of APOBEC3G catalytic domain complex with substrate ssDNA. Determined by X-ray diffraction at 1.86 Å resolution. Released 18 Jul 2018.

Method: X-ray diffraction
Resolution: 1.86 Å
Organisms: Homo sapiens, synthetic construct
Chains: 2
Atoms: 1,893
Mol. weight: 25.91 kDa
Ligands: ZN
Released: 18 Jul 2018

Explore 6BUX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6BUX contains 9 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: 9 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	197	1	1
α-helix	199-206	8
β-strand	219-228	10	2
β-strand	231-243	13	2
β-strand	245	1	3
β-strand	249	1	4
β-strand	252	1	4
β-strand	256	1	3
α-helix	258-269	12
β-strand	277-285	9	2
α-helix	286-288	3
α-helix	289-301	13
β-strand	305-313	9	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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Apolipoprotein B mRNA editing enzyme catalytic subunit 3G catalytic domain	A	protein	199	Homo sapiens	Q9HC16 (AlphaFold model)
DNA (5'-d(apaptpcpcpcpapap*a)-3')	B	DNA	9	synthetic construct

Sequence of entity 1 (A), FASTA

>6BUX_1 Apolipoprotein B mRNA editing enzyme catalytic subunit 3G catalytic domain (chains A)
GPLGSEILRHSMDPATFTFNFNNEPWVRGRHETYLCYEVERMHNDTWVKLAQRRGFLANQ
AKHKHGFLEGRHAALCFLDVIPFWKLDLDQDYRVTCFTSWSPCFSCAQEMAKFISKNKHV
SLCIKTARIYDDKGRAAEGLRTLAEAGAKISIMTYSEFKHCWDTFVDHQGAPFQPWDGLD
EHSQDLSGRLRAILQNQEN

Sequence of entity 2 (B), FASTA

>6BUX_2 DNA (5'-D(*AP*AP*TP*CP*CP*CP*AP*AP*A)-3') (chains B)
AATCCCAAA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

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

Primary citation

Crystal structure of the catalytic domain of HIV-1 restriction factor APOBEC3G in complex with ssDNA. Maiti, A., Myint, W., Kanai, T. et al. Nat Commun (2018) 9:2460-2460. DOI 10.1038/s41467-018-04872-8 · 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…
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

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