5TAR: Farnesylated and methylated kras4b

Crystal structure of farnesylated and methylated kras4b in complex with PDE-delta (crystal form II - with ordered hypervariable region). Determined by X-ray diffraction at 1.9 Å resolution. Released 2 Nov 2016.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,773
Mol. weight: 38.99 kDa
Ligands: FAR, GDP
Released: 2 Nov 2016

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

Secondary structure: helices and β-sheets

5TAR contains 13 α-helices and 17 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: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	1
α-helix	16-25	10
α-helix	35-37	3
β-strand	39-46	8	1
β-strand	49-57	9	1
α-helix	61-63	3
α-helix	65-74	10
β-strand	77-83	7	1
α-helix	87-91	5
α-helix	93-104	12
β-strand	111-116	6	1
α-helix	127-137	11
β-strand	141-143	3	1
α-helix	152-180	29
β-strand	183	1	2

Chain B: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	4-14	11
β-strand	15-24	10	3
β-strand	30-34	5	3
β-strand	45-49	5	4
α-helix	51-55	5
β-strand	58-67	10	3
β-strand	71-82	12	4
β-strand	85-97	13	4
β-strand	101-110	10	3
β-strand	111	1	2
α-helix	112-113	2
α-helix	114-116	3
α-helix	120-123	4
β-strand	127-135	9	4
β-strand	138-149	12	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
GTPase KRas	A	protein	185	Homo sapiens	P01116 (AlphaFold model)
Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta	B	protein	148	Homo sapiens	O43924 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5TAR_1 GTPase KRas (chains A)
GTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAG
QEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDL
PSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEKMSKDGKKKKKK
SKTKC

Sequence of entity 2 (B), FASTA

>5TAR_2 Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta (chains B)
AKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRE
LNFSSTEQMEKFRLEQKVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPASV
LTGNVIIETKFFDDDLLVSTSRVRLFYV

Ligands and cofactors

ID	Name	Formula	Copies
FAR	Farnesyl	C15 H26	1
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1

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

Primary citation

Structural basis of recognition of farnesylated and methylated KRAS4b by PDE delta. Dharmaiah, S., Bindu, L., Tran, T.H. et al. Proc Natl Acad Sci U S A (2016) 113:E6766-E6775. DOI 10.1073/pnas.1615316113 · PubMed

Other PDB entries of the same protein (UniProt P01116 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9IAY 0.95 Å, Structure of 10 in complex with GDP-KRAS
9IAW 1.0 Å, Structure of 5 in complex with GDP-KRAS
12XE 1.01 Å, Crystal structure of KRAS(Q61K) bound to GppNHp and ligand
8ONV 1.01 Å, KRAS-G13D in complex with BI-2493
6P0Z 1.01 Å, Crystal structure of N-acetylated KRAS (2-169) bound to GDP and Mg
9IB5 1.01 Å, Structure of 18 (BI-2493) in complex with GDP-KRAS
8AZZ 1.02 Å, KRAS-G12V in complex with BI-2865
8AZX 1.04 Å, KRAS-G12C in complex with BI-2865
8B00 1.04 Å, KRAS-G13D in complex with BI-2865
8TVK 1.04 Å, KRAS 1-169 G12C Mutant at 100k
4QL3 1.04 Å, Crystal Structure of a GDP-bound G12R Oncogenic Mutant of Human GTPase KRas
8AZV 1.05 Å, KRAS in complex with BI-2865

Browse structure collections

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