4B6D: Atypical C1 domain of MgcRacGAP

Structure of the atypical C1 domain of MgcRacGAP. Determined by X-ray diffraction at 2.2 Å resolution. Released 12 Dec 2012.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: HOMO SAPIENS
Chains: 6
Atoms: 2,932
Mol. weight: 41.82 kDa
Ligands: ZN
Released: 12 Dec 2012

Explore 4B6D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4B6D contains 12 α-helices and 34 β-strands across 6 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: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	281-282	2	1
β-strand	284	1	2
α-helix	285-287	3
β-strand	289-293	5	3
β-strand	298-299	2	4
β-strand	306-307	2	4
β-strand	312-316	5	3
β-strand	322-323	2	3
α-helix	325-330	6

Chains B, C and D: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	285-287	3
β-strand	289-293	5	5
β-strand	298-299	2	6
β-strand	306-307	2	6
β-strand	312-316	5	5
β-strand	322-323	2	5
α-helix	325-330	6

Chain E: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	285-287	3
β-strand	289-293	5	11
β-strand	298-299	2	12
β-strand	306-307	2	12
β-strand	312-316	5	11
β-strand	322-323	2	11
α-helix	325-330	6
β-strand	333	1	2

Chain F: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	284-285	2	1
α-helix	286-287	2
β-strand	289-293	5	13
β-strand	298-299	2	14
β-strand	306-307	2	14
β-strand	312-316	5	13
β-strand	322-323	2	13
α-helix	325-330	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Rac gtpase-activating protein 1	A, B, C, D, E, F	protein	61	HOMO SAPIENS	Q9H0H5 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F), FASTA

>4B6D_1 RAC GTPASE-ACTIVATING PROTEIN 1 (chains A, B, C, D, E, F)
GPLGSMRLHDFVSKTVIKPESCVPCGKRIKFGKLSLKCRDCRVVSHPECRDRCPLPCIPT
L

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	12

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

Primary citation

Centralspindlin Links the Mitotic Spindle to the Plasma Membrane During Cytokinesis. Lekomtsev, S., Su, K., Pye, V.E. et al. Nature (2012) 492:276. DOI 10.1038/NATURE11773 · PubMed

Other PDB entries of the same protein (UniProt Q9H0H5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5C2K 1.42 Å, Crystal structure of the fusion protein linked by RhoA and the GAP domain of MgcRacGAP
2OVJ 1.49 Å, The crystal structure of the human Rac GTPase activating protein 1 (RACGAP1) MgcRacGAP.
3WPQ 1.84 Å, crystal structure of the GAP domain of MgcRacGAP(S387A)
3W6R 1.9 Å, Crystal structure of the GAP domain of human MgcRacGAP
5C2J 2.5 Å, Complex structure of the GAP domain of MgcRacGAP and Cdc42
3WPS 2.7 Å, crystal structure of the GAP domain of MgcRacGAP(S387D)

Browse structure collections

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