2P2L: Rac1-GDP-Zinc Complex

Rac1-GDP-Zinc Complex. Determined by X-ray diffraction at 1.9 Å resolution. Released 1 May 2007.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 3
Atoms: 5,037
Mol. weight: 64.22 kDa
Ligands: GDP, ZN
Released: 1 May 2007

Explore 2P2L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2P2L contains 33 α-helices and 23 β-strands across 3 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: 11 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	1
α-helix	16-25	10
β-strand	33-34	2	2
α-helix	37-39	3
β-strand	40-43	4	1
β-strand	51-56	6	1
α-helix	62-64	3
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	123-131	9
α-helix	136-138	3
α-helix	139-148	10
β-strand	153-156	4	1
α-helix	165-177	13

Chain B: 11 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-10	9	3
α-helix	16-25	10
β-strand	33-34	2	1
α-helix	37-39	3
β-strand	40-44	5	3
β-strand	51-56	6	3
α-helix	62-64	3
β-strand	77-83	7	3
α-helix	87-92	6
α-helix	93-97	5
α-helix	98-104	7
β-strand	110-115	6	3
α-helix	117-119	3
α-helix	123-131	9
α-helix	136-138	3
α-helix	139-149	11
β-strand	153-156	4	3
β-strand	158	1	4
β-strand	163	1	4
α-helix	165-177	13

Chain C: 11 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-10	9	2
α-helix	16-25	10
β-strand	32-34	3	3
α-helix	37-39	3
β-strand	40-46	7	2
β-strand	49-56	8	2
α-helix	62-64	3
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	117-120	4
α-helix	125-131	7
α-helix	136-138	3
α-helix	139-148	10
β-strand	153-156	4	2
α-helix	165-177	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ras-related C3 botulinum toxin substrate 1	A, B, C	protein	188	Homo sapiens	P63000 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>2P2L_1 Ras-related C3 botulinum toxin substrate 1 (chains A, B, C)
GSKLMQAIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLW
DTAGQEDYDRLRPLSYPQTDVSLICFSLVSPASFENVRAKWYPEVRHHCPNTPIILVGTK
LDLRDDKDTIEKLKEKKLTPITYPQGLAMAKEIGAVKYLECSALTQRGLKTVFDEAIRAV
LCPPPVKK

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	3
ZN	Zinc ion	Zn	8

Primary citation

A Rac1-GDP trimer complex binds zinc with tetrahedral and octahedral coordination, displacing magnesium. Prehna, G., Stebbins, C.E. Acta Crystallogr D Biol Crystallogr (2007) 63:628-635. DOI 10.1107/S0907444907010888 · PubMed

Other PDB entries of the same protein (UniProt P63000 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9RFF 1.25 Å, Crystal Structure of Human Rac1 Fused with the Scaffold Protein POSH (residues 319-371)
9IFK 1.34 Å, Crystal structure of Kalirin/Rac1 in complex with DK-2
1MH1 1.38 Å, Small G-protein
9HU8 1.48 Å, Crystal structure of Kalirin/Rac1 in complex with MC-278.
2WKQ 1.6 Å, Structure of a photoactivatable Rac1 containing the Lov2 C450A Mutant
6X1G 1.6 Å, Crystal structure of a GEF domain from the Orientia tsutsugamushi protein OtDUB in…
5O33 1.64 Å, A structure of the GEF Kalirin DH1 domain in complex with the small GTPase Rac1
9IG1 1.65 Å, Crystal structure of Kalirin/Rac1 in complex with DK-652
9I1L 1.68 Å, Crystal structure of Kalirin/Rac1 in complex with RS-009
8I5V 1.73 Å, DOCK10 mutant L1903Y complexed with Rac1
1RYF 1.75 Å, Alternative Splicing of Rac1 Generates Rac1b, a Self-activating GTPase
1RYH 1.75 Å, Alternative Splicing of Rac1 Generates Rac1b, a Self-activating GTPase

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