2DFK: CDC42-Collybistin II complex

Crystal structure of the CDC42-Collybistin II complex. Determined by X-ray diffraction at 2.15 Å resolution. Released 2 May 2006.

Method: X-ray diffraction
Resolution: 2.15 Å
Organisms: Rattus norvegicus, Homo sapiens
Chains: 4
Atoms: 9,654
Mol. weight: 140.39 kDa
Released: 2 May 2006

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

Secondary structure: helices and β-sheets

2DFK contains 58 α-helices and 32 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: 20 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	42-43	2
α-helix	47-71	25
α-helix	72-77	6
α-helix	78-82	5
α-helix	89-96	8
α-helix	99-116	18
α-helix	122-124	3
α-helix	128-133	6
α-helix	137-139	3
α-helix	140-158	19
α-helix	162-174	13
α-helix	182-186	5
α-helix	188-205	18
α-helix	214-239	26
α-helix	241-250	10
β-strand	252	1	1
α-helix	259-261	3
β-strand	266-275	10	1
β-strand	283-290	8	1
β-strand	293-299	7	1
β-strand	307-314	8	1
α-helix	315-317	3
β-strand	318-322	5	1
α-helix	323-324	2
β-strand	326-327	2	2
β-strand	334-335	2	2
β-strand	338-343	6	1
β-strand	349-353	5	1
α-helix	357-380	24
α-helix	386-398	13

Chain B: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	3
α-helix	16-24	9
β-strand	40-46	7	3
β-strand	49-56	8	3
α-helix	68-71	4
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	117-121	5
α-helix	123-131	9
α-helix	136-138	3
α-helix	139-148	10
β-strand	154-156	3	3
α-helix	165-177	13

Chain C: 18 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	47-70	24
α-helix	71-77	7
α-helix	78-81	4
α-helix	89-96	8
α-helix	99-116	18
α-helix	122-124	3
α-helix	128-133	6
α-helix	135-139	5
α-helix	140-158	19
α-helix	162-174	13
α-helix	182-186	5
α-helix	188-205	18
α-helix	214-239	26
α-helix	241-250	10
β-strand	252	1	4
α-helix	259-261	3
β-strand	266-275	10	4
β-strand	283-290	8	4
β-strand	293-299	7	4
β-strand	307-314	8	4
α-helix	315-317	3
β-strand	318-322	5	4
β-strand	326-327	2	5
β-strand	334-335	2	5
β-strand	338-343	6	4
β-strand	349-353	5	4
α-helix	357-380	24
α-helix	386-393	8

Chain D: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	6
α-helix	16-25	10
β-strand	40-46	7	6
β-strand	49-56	8	6
α-helix	68-71	4
β-strand	77-83	7	6
α-helix	87-92	6
α-helix	93-97	5
α-helix	98-104	7
β-strand	110-115	6	6
α-helix	117-121	5
α-helix	123-131	9
α-helix	136-138	3
α-helix	139-149	11
β-strand	154-156	3	6
α-helix	165-176	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
collybistin II	A, C	protein	402	Rattus norvegicus	Q9QX73 (AlphaFold model)
cell division cycle 42 isoform 1	B, D	protein	194	Homo sapiens	P60953 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>2DFK_1 collybistin II (chains A, C)
MLWVNQEDGVEEGPSDVQNGHLDPNSDCLCLGRPLQNRDQMRANVINEIMSTERHYIKHL
KDICEGYLKQCRKRRDMFSDEQLKVIFGNIEDIYRFQMGFVRDLEKQYNNDDPHLSEIGP
CFLEHQDGFWIYSEYCNNHLDACMELSKLMKDSRYQHFFEACRLLQQMIDIAIDGFLLTP
VQKICKYPLQLAELLKYTAQDHSDYRYVAAALAVMRNVTQQINERKRRLENIDKIAQWQA
SVLDWEGDDILDRSSELIYTGEMAWIYQPYGRNQQRVFFLFDHQMVLCKKDLIRRDILYY
KGRIDMDKYEVIDIEDGRDDDFNVSMKNAFKLHNKETEEVHLFFAKKLEEKIRWLRAFRE
ERKMVQEDEKIGFEISENQKRQAAMTVRKASKQKVTQRKWHY

Sequence of entity 2 (B, D), FASTA

>2DFK_2 cell division cycle 42 isoform 1 (chains B, D)
GSHMQTIKCVVVGDGAVGKTCLLISYTTNKFPSEYVPTVFDNYAVTVMIGGEPYTLGLFD
TAGQEDYDRLRPLSYPQTDVFLVCFSVVSPSSFENVKEKWVPEITHHCPKTPFLLVGTQI
DLRDDPSTIEKLAKNKQKPITPETAEKLARDLKAVKYVECSALTQKGLKNVFDEAILAAL
EPPEPKKSRRCVLL

Primary citation

The Crystal Structure of Cdc42 in Complex with Collybistin II, a Gephyrin-interacting Guanine Nucleotide Exchange Factor. Xiang, S., Kim, E.Y., Connelly, J.J. et al. J Mol Biol (2006) 359:35-46. DOI 10.1016/j.jmb.2006.03.019 · PubMed

Other PDB entries of the same protein (UniProt Q9QX73 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4MT7 3.5 Å, Crystal structure of collybistin I
4MT6 5.5 Å, Crystal structure of closed inactive collybistin

Browse structure collections

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