7KDC: The complex between RhoD and the Plexin B2 RBD

The complex between RhoD and the Plexin B2 RBD. Determined by X-ray diffraction at 3.1 Å resolution. Released 28 Jul 2021.

Method: X-ray diffraction
Resolution: 3.1 Å
Organisms: Homo sapiens, Mus musculus
Chains: 4
Atoms: 4,458
Mol. weight: 67.15 kDa
Ligands: MG, GNP
Released: 28 Jul 2021

Explore 7KDC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7KDC contains 29 α-helices and 30 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: 12 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	16-24	9	1
α-helix	30-38	9
β-strand	52-60	9	1
β-strand	63-71	9	1
α-helix	76-78	3
α-helix	82-85	4
β-strand	91-97	7	1
α-helix	101-106	6
α-helix	107-111	5
α-helix	112-117	6
β-strand	124-129	6	1
α-helix	131-135	5
α-helix	137-145	9
α-helix	150-152	3
α-helix	153-163	11
β-strand	167-170	4	1
β-strand	172	1	2
α-helix	173-175	3
β-strand	177	1	2
α-helix	179-192	14

Chain B: 11 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	17-24	8	3
α-helix	30-38	9
β-strand	51-60	10	3
β-strand	63-72	10	3
α-helix	76-78	3
α-helix	82-85	4
β-strand	91-97	7	3
α-helix	101-106	6
α-helix	107-111	5
α-helix	112-117	6
β-strand	124-129	6	3
α-helix	131-135	5
α-helix	137-145	9
α-helix	153-163	11
β-strand	167-170	4	3
β-strand	172	1	4
α-helix	173-175	3
β-strand	177	1	4
α-helix	179-192	14

Chain C: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	1466-1473	8	5
β-strand	1481-1486	6	5
β-strand	1490	1	6
α-helix	1491-1502	12
α-helix	1514-1516	3
β-strand	1517-1521	5	7
β-strand	1528-1529	2	7
α-helix	1544-1547	4
β-strand	1548	1	8
β-strand	1559-1564	6	7

Chain D: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	1466-1473	8	7
β-strand	1481-1486	6	7
β-strand	1490	1	8
α-helix	1491-1503	13
α-helix	1514-1516	3
β-strand	1517-1521	5	5
β-strand	1528-1530	3	5
α-helix	1544-1547	4
β-strand	1548	1	6
β-strand	1559-1564	6	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Rho-related GTP-binding protein RhoD	A, B	protein	191	Homo sapiens	O00212 (AlphaFold model)
Plexin-B2	C, D	protein	103	Mus musculus	B2RXS4 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7KDC_1 Rho-related GTP-binding protein RhoD (chains A, B)
GPHMGEEAPPGVRSVKVVLVGDGGCGKTSLLMVFADGAFPESYTPTVFERYMVNLQVKGK
PVHLHIWDTAGLDDYDRLRPLFYPDASVLLLCFDVTSPNSFDNIFNRWYPEVNHFCKKVP
IIVVGCKTDLRKDKSLVNKLRRNGLEPVTYHRGQEMARSVGAVAYLECSARLHDNVHAVF
QEAAEVALSSR

Sequence of entity 2 (C, D), FASTA

>7KDC_2 Plexin-B2 (chains C, D)
EYAPLTVSVIVQDEGIDAIPVKVLNCDTISQVKEKIIDQVYRTQPCSCWPKPDSVVLEWR
PGSTAQILSDLDLTSQREGRWKRINTLMHYNVRDGATLILSKV

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	4
GNP	Phosphoaminophosphonic acid-guanylate ester	C10 H17 N6 O13 P3	2

Primary citation

A putative structural mechanism underlying the antithetic effect of homologous RND1 and RhoD GTPases in mammalian plexin regulation. Liu, Y., Ke, P., Kuo, Y.C. et al. Elife (2021) 10. DOI 10.7554/eLife.64304 · PubMed

Other PDB entries of the same protein (UniProt O00212 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2J1L 2.5 Å, Crystal Structure of Human Rho-related GTP-binding protein RhoD

Browse structure collections

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