3LVR: ASAP3

The crystal structure of ASAP3 in complex with Arf6 in transition state soaked with Calcium. Determined by X-ray diffraction at 3.38 Å resolution. Released 9 Jun 2010.

Method: X-ray diffraction
Resolution: 3.38 Å
Organisms: Homo sapiens, synthetic construct
Chains: 1
Atoms: 3,298
Mol. weight: 55.48 kDa
Ligands: ZN, MG, GDP, AF3
Released: 9 Jun 2010

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

Secondary structure: helices and β-sheets

3LVR contains 21 α-helices and 15 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 E: 21 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	426-433	8
β-strand	440	1	1
β-strand	447	1	1
β-strand	451-453	3	2
β-strand	458-460	3	2
α-helix	462-471	10
β-strand	478-480	3	2
α-helix	488-491	4
α-helix	492-496	5
α-helix	499-506	8
α-helix	524-532	9
α-helix	533-537	5
α-helix	548-557	10
α-helix	560-568	9
β-strand	576-577	2	3
β-strand	587-588	2	3
α-helix	589-595	7
α-helix	602-611	10
α-helix	625-631	7
α-helix	635-643	9
α-helix	658-664	7
α-helix	670-676	7
β-strand	13-19	7	4
α-helix	26-35	10
β-strand	47-53	7	4
β-strand	58-64	7	4
α-helix	68-70	3
α-helix	74-77	4
β-strand	83-89	7	4
α-helix	96-107	12
β-strand	116-122	7	4
α-helix	132-138	7
β-strand	148-153	6	4
β-strand	155	1	5
β-strand	160	1	5
α-helix	162-172	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3, ADP-ribosylation factor 6	E	protein	497	Homo sapiens, synthetic construct	P62330 (AlphaFold model), Q8TDY4 (AlphaFold model)

Sequence of entity 1 (E), FASTA

>3LVR_1 Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3, ADP-ribosylation factor 6 (chains E)
GHDGEPHDLTKLLIAEVKSRPGNSQCCDCGAADPTWLSTNLGVLTCIQCSGVHRELGVRF
SRMQSLTLDLLGPSELLLALNMGNTSFNEVMEAQLPSHGGPKPSAESDMGTRRDYIMAKY
VEHRFARRCTPEPQRLWTAICNRDLLSVLEAFANGQDFGQPLPGPDAQAPEELVLHLAVK
VANQASLPLVDFIIQNGGHLDAKAADGNTALHYAALYNQPDCLKLLLKGRALVGTVNEAG
ETALDIARKKHHKECEELLEQAQAGTFAFPLHVDYSWVISTENLSSDSSLSSPSALNSLS
SPSALNSTASNSPGIEGLSNKEMRILMLGLDAAGKTTILYKLKLGQSVTTIPTVGFNVET
VTYKNVKFNVWDVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDRE
MRDAIILIFANKQDLPDAMKPHEIQEKLGLTRIRDRNWYVQPSCATSGDGLYEGLTWLTS
NYKSKLAAALEHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
MG	Magnesium ion	Mg	1
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
AF3	Aluminum fluoride	Al F3	1
CA	Calcium ion	Ca	1

Primary citation

The structure of an Arf-ArfGAP complex reveals a Ca2+ regulatory mechanism. Ismail, S.A., Vetter, I.R., Sot, B. et al. Cell (2010) 141:812-821. DOI 10.1016/j.cell.2010.03.051 · 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
3N5C 1.82 Å, Crystal Structure of Arf6DELTA13 complexed with GDP
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

Browse structure collections

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