1NF3: G25K GTP-binding protein, placental isoform

Structure of Cdc42 in a complex with the GTPase-binding domain of the cell polarity protein, Par6. Determined by X-ray diffraction at 2.1 Å resolution. Released 4 Mar 2003.

Method: X-ray diffraction
Resolution: 2.1 Å
Organisms: Homo sapiens, Mus musculus
Chains: 4
Atoms: 5,395
Mol. weight: 72.58 kDa
Ligands: GNP, MG
Released: 4 Mar 2003

Explore 1NF3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1NF3 contains 30 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: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	1
α-helix	16-25	10
β-strand	37-46	10	1
β-strand	49-58	10	1
α-helix	62-71	10
β-strand	77-83	7	1
α-helix	87-92	6
α-helix	93-97	5
α-helix	98-104	7
β-strand	110-115	6	1
α-helix	117-119	3
α-helix	123-130	8
α-helix	136-138	3
α-helix	139-149	11
β-strand	154-156	3	1
α-helix	165-177	13

Chain B: 11 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	2
α-helix	16-25	10
β-strand	37-46	10	2
β-strand	49-58	10	2
α-helix	62-71	10
β-strand	77-83	7	2
α-helix	87-92	6
α-helix	93-97	5
α-helix	98-104	7
β-strand	110-115	6	2
α-helix	117-121	5
α-helix	123-130	8
α-helix	136-138	3
α-helix	139-149	11
β-strand	154-156	3	2
α-helix	165-177	13
α-helix	183-186	4

Chain C: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	133	1	1
β-strand	137-146	10	1
β-strand	156-160	5	1
β-strand	171-182	12	1
β-strand	185-197	13	1
α-helix	202-206	5
α-helix	213	1
β-strand	214-218	5	1
β-strand	221-222	2	1
α-helix	228-237	10
β-strand	242-247	6	1
α-helix	248-252	5

Chain D: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	133	1	2
β-strand	137-146	10	2
β-strand	156-160	5	2
β-strand	171-181	11	2
β-strand	186-197	12	2
α-helix	202-206	5
α-helix	213	1
β-strand	214-218	5	2
β-strand	221-222	2	2
α-helix	228-238	11
α-helix	239-241	3
β-strand	242-247	6	2
α-helix	248-252	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
G25K GTP-binding protein, placental isoform	A, B	protein	195	Homo sapiens	P60953 (AlphaFold model)
Par-6B	C, D	protein	128	Mus musculus	Q9JK83 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>1NF3_1 G25K GTP-binding protein, placental isoform (chains A, B)
GAMGIQTIKCVVVGDGAVGKTCLLISYTTNKFPSEYVPTVFDNYAVTVMIGGEPYTLGLF
DTAGLEDYDRLRPLSYPQTDVFLVCFSVVSPSSFENVKEKWVPEITHHCPKTPFLLVGTQ
IDLRDDPSTIEKLAKNKQKPITPETAEKLARDLKAVKYVECSALTQKGLKNVFDEAILAA
LEPPEPKKSRRCVLL

Sequence of entity 2 (C, D), FASTA

>1NF3_2 PAR-6B (chains C, D)
RKKPHIVISMPQDFRPVSSIIDVDILPETHRRVRLCKYGTEKPLGFYIRDGSSVRVTPHG
LEKVPGIFISRLVPGGLAQSTGLLAVNDEVLEVNGIEVSGKSLDQVTDMMIANSRNLIIT
VRPANQRN

Ligands and cofactors

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

Primary citation

Structure of Cdc42 in a complex with the GTPase-binding domain of the cell polarity protein, Par6. Garrard, S.M., Capaldo, C.T., Gao, L. et al. EMBO J (2003) 22:1125-1133. DOI 10.1093/emboj/cdg110 · PubMed

Other PDB entries of the same protein (UniProt P60953 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2NGR 1.9 Å, Transition state complex for GTP hydrolysis by CDC42: comparisons of the high resolution…
4JS0 1.9 Å, Complex of Cdc42 with the CRIB-PR domain of IRSp53
6SUP 2.0 Å, Crystal Structure of TcdB2-TccC3-Cdc42
3VHL 2.08 Å, Crystal structure of the DHR-2 domain of DOCK8 in complex with Cdc42 (T17N mutant)
1GRN 2.1 Å, Crystal structure of the CDC42/CDC42GAP/ALF3 complex.
2DFK 2.15 Å, Crystal structure of the CDC42-Collybistin II complex
2WM9 2.2 Å, Structure of the complex between DOCK9 and Cdc42.
2WMO 2.2 Å, Structure of the complex between DOCK9 and Cdc42.
1GZS 2.3 Å, Crystal structure of the complex between the gef domain of the salmonella typhimurium…
1KI1 2.3 Å, Guanine Nucleotide Exchange Region of Intersectin in Complex with Cdc42
3GCG 2.3 Å, crystal structure of MAP and CDC42 complex
4ITR 2.3 Å, Crystal Structure of IbpAFic2-H3717A in complex with adenylylated Cdc42

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