1C1Y: Rap.gmppnp

Crystal structure of rap.gmppnp in complex with the ras-binding-domain of C-RAF1 kinase (RAFRBD). Determined by X-ray diffraction at 1.9 Å resolution. Released 2 Aug 1999.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,151
Mol. weight: 28.43 kDa
Ligands: MG, GTP, CA
Released: 2 Aug 1999

Explore 1C1Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1C1Y contains 12 α-helices and 15 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, 8 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	1
α-helix	16-24	9
β-strand	37-45	9	1
β-strand	50-58	9	1
α-helix	59	1
α-helix	67-74	8
β-strand	77-83	7	1
α-helix	87-91	5
α-helix	93-104	12
β-strand	111-116	6	1
α-helix	121-123	3
α-helix	128-137	10
β-strand	142-145	4	1
β-strand	147	1	2
β-strand	152	1	2
α-helix	154-165	12

Chain B: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	57-62	6	1
β-strand	66-71	6	1
β-strand	77	1	3
α-helix	78-87	10
α-helix	93-95	3
β-strand	96-102	7	1
α-helix	103-105	3
β-strand	108-112	5	1
β-strand	117	1	3
α-helix	118-121	4
β-strand	125-130	6	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ras-related protein rap-1A	A	protein	167	Homo sapiens	P62834 (AlphaFold model)
Proto-oncogene serine/threonine protein kinase raf-1	B	protein	77	Homo sapiens	P04049 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1C1Y_1 RAS-RELATED PROTEIN RAP-1A (chains A)
MREYKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDCQQCMLEILDTAG
TEQFTAMRDLYMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTEDVPMILVGNKCDL
EDERVVGKEQGQNLARQWCNCAFLESSAKSKINVNEIFYDLVRQINR

Sequence of entity 2 (B), FASTA

>1C1Y_2 PROTO-ONCOGENE SERINE/THREONINE PROTEIN KINASE RAF-1 (chains B)
SNTIRVFLPNKQRTVVNVRNGMSLHDCLMKALKVRGLQPECCAVFRLLHEHKGKKARLDW
NTDAASLIGEELQVDFL

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1
CA	Calcium ion	Ca	1

Primary citation

The 2.2 A crystal structure of the Ras-binding domain of the serine/threonine kinase c-Raf1 in complex with Rap1A and a GTP analogue. Nassar, N. Nature (1995) 375:554-560. DOI 10.1038/375554a0 · PubMed

Other PDB entries of the same protein (UniProt P62834 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4KVG 1.65 Å, Crystal structure of RIAM RA-PH domains in complex with GTP bound Rap1
3KUC 1.92 Å, Complex of Rap1A(E30D/K31E)GDP with RafRBD(A85K/N71R)
1GUA 2.0 Å, Human RAP1A, residues 1-167, double mutant (E30D,K31E) complexed with gppnhp and the…

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