5KDO: PDB entry 5KDO

Heterotrimeric complex of the 4 alanine insertion variant of the Gi alpha1 subunit and the Gbeta1-Ggamma1. Determined by X-ray diffraction at 1.9 Å resolution. Released 3 Aug 2016.

Method: X-ray diffraction
Resolution: 1.9 Å
Organisms: Rattus norvegicus, Bos taurus
Chains: 3
Atoms: 6,086
Mol. weight: 87.1 kDa
Ligands: GDP
Released: 3 Aug 2016

Explore 5KDO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5KDO contains 31 α-helices and 35 β-strands across 3 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: 22 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	8-31	24
β-strand	34-40	7	1
α-helix	46-57	12
α-helix	63-67	5
α-helix	70-91	22
α-helix	100-113	14
α-helix	114-115	2
α-helix	121-132	12
α-helix	134-140	7
α-helix	143-145	3
α-helix	152-156	5
α-helix	159-162	4
α-helix	171-176	6
β-strand	185-190	6	1
β-strand	195-200	6	1
α-helix	208-210	3
α-helix	212-215	4
β-strand	220-226	7	1
α-helix	227-231	5
α-helix	232-234	3
α-helix	242-254	13
α-helix	257-259	3
β-strand	263-269	7	1
α-helix	271-280	10
α-helix	283-285	3
α-helix	296-308	13
β-strand	319-323	5	1
α-helix	329-344	16

Chain B: 3 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	3-24	22
α-helix	30-33	4
α-helix	38-39	2
β-strand	43	1	2
β-strand	47-51	5	3
β-strand	58-63	6	4
β-strand	69-74	6	4
β-strand	78-83	6	4
β-strand	88-94	7	4
β-strand	100-105	6	5
β-strand	111-116	6	5
β-strand	121-125	5	5
β-strand	134-139	6	5
β-strand	146-153	8	6
β-strand	156-161	6	6
β-strand	166-170	5	6
β-strand	175-180	6	6
β-strand	187-192	6	7
β-strand	198-203	6	7
β-strand	208-212	5	7
β-strand	217-222	6	7
β-strand	229-234	6	8
β-strand	240-245	6	8
β-strand	250-254	5	8
β-strand	259-264	6	8
β-strand	273-278	6	2
β-strand	284-289	6	2
β-strand	294-298	5	2
β-strand	304-308	5	2
β-strand	315-320	6	3
β-strand	327-331	5	3
β-strand	336-339	4	3

Chain G: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	11-25	15
α-helix	30-32	3
α-helix	33-45	13
α-helix	48-50	3
α-helix	52-55	4
α-helix	59-61	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	protein	358	Rattus norvegicus	P10824 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	340	Bos taurus	P62871 (AlphaFold model)
Guanine nucleotide-binding protein G(T) subunit gamma-T1	G	protein	74	Bos taurus	P02698 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5KDO_1 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDAARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQAAAAFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 2 (B), FASTA

>5KDO_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYA
MHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNI
CSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTF
TGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNA
FATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDAL
KADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (G), FASTA

>5KDO_3 Guanine nucleotide-binding protein G(T) subunit gamma-T1 (chains G)
MPVINIEDLTEKDKLKMEVDQLKKEVTLERMLVSKCCEEFRDYVEERSGEDPLVKGIPED
KNPFKELKGGCVIS

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1

Primary citation

A Conserved Hydrophobic Core in G alpha i1 Regulates G Protein Activation and Release from Activated Receptor. Kaya, A.I., Lokits, A.D., Gilbert, J.A. et al. J Biol Chem (2016) 291:19674-19686. DOI 10.1074/jbc.M116.745513 · PubMed

Other PDB entries of the same protein (UniProt P10824 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1CIP 1.5 Å, Gi-alpha-1 subunit of guanine nucleotide-binding protein complexed with a GTP analogue
1SVS 1.5 Å, Structure of the K180P mutant of Gi alpha subunit bound to GppNHp.
4N0D 1.55 Å, Crystal structure of the K345L variant of the Gi alpha1 subunit bound to GTPgammaS
1AS0 2.0 Å, GTP-gamma-S bound G42V GIA1
1GIA 2.0 Å, Structure of active conformations of GIA1 and the mechanism of GTP hydrolysis
1SVK 2.0 Å, Structure of the K180P mutant of Gi alpha subunit bound to AlF4 and GDP
4PAQ 2.0 Å, A conserved phenylalanine as relay between the 5 helix and the GDP binding region of…
4PAO 2.0 Å, A conserved phenylalanine as relay between the 5 helix and the GDP binding region of…
1FQJ 2.02 Å, Crystal structure of the heterotrimeric complex of the rgs domain of RGS9, the gamma…
6M8H 2.07 Å, Crystal Structure of the R208Q mutant of G(i) subunit alpha-1
1BH2 2.1 Å, A326S mutant of an inhibitory alpha subunit
4N0E 2.1 Å, Crystal structure of the K345L variant of the Gi alpha1 subunit bound to GDP

Browse structure collections

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