3N5C: Arf6DELTA13

Crystal Structure of Arf6DELTA13 complexed with GDP. Determined by X-ray diffraction at 1.82 Å resolution. Released 18 Aug 2010.

Method: X-ray diffraction
Resolution: 1.82 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,731
Mol. weight: 38.34 kDa
Ligands: GDP
Released: 18 Aug 2010

Explore 3N5C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3N5C contains 17 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: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	15-21	7	1
α-helix	26-35	10
β-strand	58-64	7	1
α-helix	65-67	3
β-strand	75	1	2
β-strand	83-89	7	1
α-helix	93-95	3
α-helix	96-107	12
α-helix	110-112	3
β-strand	116-122	7	1
α-helix	129-131	3
α-helix	132-138	7
α-helix	141-143	3
β-strand	149-153	5	1
β-strand	155	1	3
β-strand	160	1	3
α-helix	162-173	12

Chain B: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	15-21	7	2
α-helix	26-40	15
α-helix	52-55	4
β-strand	58-64	7	2
β-strand	75	1	1
β-strand	83-89	7	2
α-helix	96-107	12
α-helix	110-112	3
β-strand	116-122	7	2
α-helix	129-131	3
α-helix	132-138	7
α-helix	141-143	3
β-strand	149-153	5	2
β-strand	155	1	4
β-strand	160	1	4
α-helix	162-172	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ADP-ribosylation factor 6	A, B	protein	162	Homo sapiens	P62330 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3N5C_1 ADP-ribosylation factor 6 (chains A, B)
MRILMLGLDAAGKTTILYKLKLGQSVTTIPTVGFNVETVTYKNVKFNVWDVGGQDKIRPL
WRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFANKQDLPDAMKPH
EIQEKLGLTRIRDRNWYVQPSCATSGDGLYEGLTWLTSNYKS

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2

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

Primary citation

SAXS and X-ray crystallography suggest an unfolding model for the GDP/GTP conformational switch of the small GTPase Arf6. Biou, V., Aizel, K., Roblin, P. et al. J Mol Biol (2010) 402:696-707. DOI 10.1016/j.jmb.2010.08.002 · PubMed

Other PDB entries of the same protein (UniProt P62330 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2A5D 1.8 Å, Structural basis for the activation of cholera toxin by human ARF6-GTP
4KAX 1.85 Å, Crystal structure of the Grp1 PH domain in complex with Arf6-GTP
2W83 1.93 Å, Crystal structure of the ARF6 GTPase in complex with a specific effector, JIP4
6PAU 1.93 Å, Structure of Human NMT2 with myristoyl-lysine peptide and CoA products
2A5F 2.02 Å, Cholera toxin A1 subunit bound to its substrate, NAD+, and its human protein activator,…
7RK3 2.05 Å, Crystal structure of human N-myristoyltransferase 1 fragment (residues 109-496) bound to…
1E0S 2.28 Å, small G protein Arf6-GDP
3PCR 2.5 Å, Structure of EspG-Arf6 complex
6PAV 2.52 Å, Structure of Human NMT1 with products CoA and myristoyl-lysine peptide with acetylated…
2A5G 2.66 Å, Cholera toxin A1 subunit bound to ARF6(Q67L)
2J5X 2.8 Å, Structure of the small G protein ARF6 in complex with gtpgammas
3LVQ 3.38 Å, The crystal structure of ASAP3 in complex with Arf6 in transition state

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