5QQD: Ras-related C3 botulinum toxin substrate 1

PanDDA analysis group deposition -- Crystal Structure of Kalirin/Rac1 in complex with Z56880342. Determined by X-ray diffraction at 1.91 Å resolution. Released 18 Dec 2019.

Method: X-ray diffraction
Resolution: 1.91 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,128
Mol. weight: 41.3 kDa
Ligands: JGA
Released: 18 Dec 2019

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

Secondary structure: helices and β-sheets

5QQD contains 28 α-helices and 6 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: 11 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	1
α-helix	12-14	3
α-helix	16-25	10
β-strand	40-46	7	1
β-strand	49-56	8	1
α-helix	68-71	4
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	139-149	11
β-strand	153-156	4	1
α-helix	165-174	10

Chain B: 17 helices, 0 β-strands

Element	Residues	Length
α-helix	1233-1255	23
α-helix	1256-1260	5
α-helix	1261-1264	4
α-helix	1272-1274	3
α-helix	1278-1282	5
α-helix	1285-1291	7
α-helix	1292-1296	5
α-helix	1297-1302	6
α-helix	1307-1309	3
α-helix	1311-1316	6
α-helix	1318-1322	5
α-helix	1323-1329	7
α-helix	1331-1341	11
α-helix	1345-1353	9
α-helix	1359-1370	12
α-helix	1373-1383	11
α-helix	1389-1407	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ras-related C3 botulinum toxin substrate 1	A	protein	178	Homo sapiens	P63000 (AlphaFold model)
Kalirin	B	protein	182	Homo sapiens	O60229 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5QQD_1 Ras-related C3 botulinum toxin substrate 1 (chains A)
SMQAIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTA
GQEDYDRLRPLSYPQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDL
RDDKDTIEKLKEKKLTPITYPQGLAMAKEIGAVKYLECSALTQRGLKTVFDEAIRAVL

Sequence of entity 2 (B), FASTA

>5QQD_2 Kalirin (chains B)
SMRKKEFIMAELLQTEKAYVRDLHECLETYLWEMTSGVEEIPPGILNKEHIIFGNIQEIY
DFHNNIFLKELEKYEQLPEDVGHCFVTWADKFQMYVTYCKNKPDSNQLILEHAGTFFDEI
QQRHGLANSISSYLIKPVQRVTKYQLLLKELLTCCEEGKGELKDGLEVMLSVPKKANDAM
HV

Ligands and cofactors

ID	Name	Formula	Copies
JGA	N-ethyl-N'-(5-methyl-1,2-oxazol-3-yl)urea	C7 H11 N3 O2	1

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

Primary citation

PanDDA analysis group deposition. Gray, J.L., Krojer, T., Talon, R. et al. To be published.

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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