5C2K: PDB entry 5C2K

Crystal structure of the fusion protein linked by RhoA and the GAP domain of MgcRacGAP. Determined by X-ray diffraction at 1.42 Å resolution. Released 22 Jun 2016.

Method: X-ray diffraction
Resolution: 1.42 Å
Organism: Homo sapiens
Chains: 1
Atoms: 3,739
Mol. weight: 46.62 kDa
Ligands: GDP, AF3, MG
Released: 22 Jun 2016

Explore 5C2K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5C2K contains 26 α-helices and 8 β-strands across 1 chain. 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: 26 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3	1
β-strand	4-12	9	1
α-helix	18-27	10
β-strand	39-48	10	1
β-strand	51-60	10	1
α-helix	64-66	3
α-helix	70-73	4
β-strand	79-85	7	1
α-helix	89-94	6
α-helix	95-99	5
α-helix	100-106	7
β-strand	112-117	6	1
α-helix	119-121	3
α-helix	125-132	8
α-helix	138-140	3
α-helix	141-151	11
β-strand	155-158	4	1
α-helix	167-182	16
α-helix	213-215	3
β-strand	217	1	2
β-strand	225	1	2
α-helix	226-238	13
α-helix	252-265	14
α-helix	268-269	2
α-helix	271-273	3
α-helix	277-289	13
α-helix	301-309	9
α-helix	313-326	14
α-helix	329-347	19
α-helix	355-362	8
α-helix	363-367	5
α-helix	376-383	8
α-helix	385-394	10
α-helix	398-403	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transforming protein RhoA,Rac GTPase-activating protein 1	A	protein	415	Homo sapiens	P61586 (AlphaFold model), Q9H0H5 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5C2K_1 Transforming protein RhoA,Rac GTPase-activating protein 1 (chains A)
GSSGSSGMAAIRKKLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYVADIEVDGKQV
ELALWDTAGQEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPII
LVGNKKDLRNDEHTRRELAKMKQEPVKPEEGRDMANRIGAFGYMECSAKTKDGVREVFEM
ATRAALQARRGKKKSGCLVLSGSSGSSGSSGSSGIGEGMLADFVSQTSPMIPSIVVHCVN
EIEQRGLTETGLYRIDGCDRTVKELKEKFLRVKTVPLLSKVDDIHAICSLLKDFLRNLKE
PLLTFRLNRAFMEAAEITDEDNSIAAMYQAVGELPQANRDTLAFLMIHLQRVAQSPHTKM
DVANLAKVFGPTIVAHAVPNPDPVTMSQDIKRQPKVVERLLSLPLEYWSQFMMVE

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
AF3	Aluminum fluoride	Al F3	1
MG	Magnesium ion	Mg	1

Primary citation

Structural basis for the effects of Ser387 phosphorylation of MgcRacGAP on its GTPase-activating activities for CDC42 and RHOA. Murayama, K., Kato-Murayama, M., Hosaka, T. et al. J Struct Biol (2024) 216:108151-108151. DOI 10.1016/j.jsb.2024.108151 · PubMed

Other PDB entries of the same protein (UniProt P61586 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6V6U 1.16 Å, Crystal structure of RhoA-GDP with novel Switch I conformation
5C4M 1.3 Å, RhoA GDP with novel switch II conformation
7G83 1.31 Å, ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with Z108545814
7G8T 1.39 Å, ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with Z1273312142
6V6M 1.39 Å, Crystal structure of an inactive state of GMPPNP-bound RhoA
6V6V 1.4 Å, Crystal structure of oncogenic RhoA mutant G14V complexed with GDP
8BNT 1.4 Å, The DH domain of ARHGEF2 bound to RhoA
8FPW 1.4 Å, Crystal structure of tumor related RhoA mutant A161V in complex with GDP
8GI6 1.4 Å, Crystal structure of RhoA mutant L69R complexed with GDP
6BCB 1.4 Å, A Complex between PH Domain of p114RhoGEF and Activated RhoA Bound to a GTP Analog
7G82 1.41 Å, ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with Z1079512010
7G8B 1.42 Å, ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with Z100643660

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