5KHO: Rasip1 RA domain

Rasip1 RA domain in complex with Rap1B. Determined by X-ray diffraction at 2.78 Å resolution. Released 19 Oct 2016.

Method: X-ray diffraction
Resolution: 2.78 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,132
Mol. weight: 71.92 kDa
Ligands: MG, GNP
Released: 19 Oct 2016

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

Secondary structure: helices and β-sheets

5KHO contains 24 α-helices and 28 β-strands across 4 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: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	146-152	7	1
β-strand	159-166	8	1
α-helix	172-180	9
α-helix	199-201	3
β-strand	202-209	8	1
β-strand	225-228	4	1
α-helix	229-230	2
α-helix	235-241	7
β-strand	242-244	3	2
β-strand	249-256	8	1
α-helix	257-264	8

Chain B: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	147-151	5	3
β-strand	159-165	7	3
α-helix	172-183	12
α-helix	198-201	4
β-strand	202-209	8	3
β-strand	225-228	4	3
α-helix	235-241	7
β-strand	242-244	3	2
α-helix	245	1
β-strand	249-256	8	3
α-helix	257-265	9

Chain C: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	1
α-helix	16-24	9
β-strand	38-45	8	1
β-strand	50-57	8	1
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	121-123	3
α-helix	128-137	10
β-strand	142-146	5	1
β-strand	147	1	4
β-strand	152	1	4
α-helix	154-165	12

Chain D: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	3
α-helix	16-25	10
β-strand	38-45	8	3
β-strand	50-57	8	3
α-helix	68-74	7
β-strand	77-83	7	3
α-helix	87-91	5
α-helix	93-103	11
β-strand	111-116	6	3
α-helix	121-123	3
α-helix	128-137	10
β-strand	142-145	4	3
β-strand	147	1	5
β-strand	152	1	5
α-helix	154-165	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ras-interacting protein 1	A, B	protein	156	Homo sapiens	Q5U651 (AlphaFold model)
Ras-related protein Rap-1b	C, D	protein	167	Homo sapiens	P61224 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5KHO_1 Ras-interacting protein 1 (chains A, B)
GAMGEPPLATRATAPPGVLKIFGAGLASGANYKSVLATARSTARELVAEALERYGLAGSP
GGGPGESSCVDAFALCDALGRPAAAGVGSGEWRAEHLRVLGDSERPLLVQELWRARPGWA
RRFELRGREEARRLEQEAFGAADSEGTGAPSWRPQK

Sequence of entity 2 (C, D), FASTA

>5KHO_2 Ras-related protein Rap-1b (chains C, D)
MREYKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDAQQCMLEILDTAG
TEQFTAMRDLYMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTDDVPMILVGNKCDL
EDERVVGKEQGQNLARQWNNCAFLESSAKSKINVNEIFYDLVRQINR

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
GNP	Phosphoaminophosphonic acid-guanylate ester	C10 H17 N6 O13 P3	2

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

Primary citation

Structural Basis of Dimeric Rasip1 RA Domain Recognition of the Ras Subfamily of GTP-Binding Proteins. Gingras, A.R., Puzon-McLaughlin, W., Bobkov, A.A. et al. Structure (2016) 24:2152-2162. DOI 10.1016/j.str.2016.10.001 · PubMed

Other PDB entries of the same protein (UniProt Q5U651 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5KHQ 2.8 Å, Rasip1 RA domain

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