5HZK: Cell division control protein 42 homolog

Crystal structure of photoinhibitable Intersectin1 containing wildtype LOV2 domain in complex with Cdc42. Determined by X-ray diffraction at 3.3 Å resolution. Released 21 Dec 2016.

Method: X-ray diffraction
Resolution: 3.3 Å
Organisms: Homo sapiens, Avena sativa
Chains: 4
Atoms: 10,477
Mol. weight: 160.53 kDa
Ligands: FMN, GDP
Released: 21 Dec 2016

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

Secondary structure: helices and β-sheets

5HZK contains 61 α-helices and 51 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: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	1
α-helix	16-24	9
α-helix	28-30	3
β-strand	40-46	7	1
β-strand	49-57	9	1
α-helix	68-70	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	123-130	8
α-helix	139-148	10
β-strand	154-156	3	1
α-helix	165-175	11

Chain B: 21 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	1233-1259	27
α-helix	1260-1264	5
α-helix	1265-1270	6
α-helix	1275-1281	7
α-helix	1285-1312	28
β-strand	1319-1323	5	2
β-strand	1332-1335	4	2
α-helix	1337-1343	7
α-helix	1347-1349	3
α-helix	1355-1358	4
β-strand	1359	1	2
β-strand	1364	1	3
α-helix	1365-1376	12
β-strand	1381-1388	8	2
β-strand	1394-1405	12	2
β-strand	1411-1418	8	2
β-strand	1420-1421	2	2
α-helix	1427-1447	21
α-helix	1453-1455	3
α-helix	1459-1465	7
α-helix	1466-1468	3
α-helix	1471-1491	21
α-helix	1494-1503	10
α-helix	1507-1509	3
α-helix	1514-1517	4
α-helix	1519-1526	8
α-helix	1528-1536	9
α-helix	1546-1580	35
β-strand	1584	1	4
β-strand	1597	1	5
β-strand	1603	1	5
β-strand	1606-1614	9	6
β-strand	1620-1626	7	6
β-strand	1629-1634	6	6
β-strand	1657	1	4
β-strand	1663-1664	2	6
β-strand	1668-1669	2	7
β-strand	1684-1687	4	7
β-strand	1690-1693	4	7
β-strand	1694-1695	2	6
α-helix	1699-1720	22

Chain C: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	3
α-helix	16-24	9
α-helix	28-30	3
β-strand	40-46	7	3
β-strand	49-57	9	3
α-helix	68-70	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	123-130	8
α-helix	139-148	10
β-strand	154-156	3	3
α-helix	165-176	12

Chain D: 20 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	1233-1259	27
α-helix	1260-1264	5
α-helix	1265-1270	6
α-helix	1275-1281	7
α-helix	1285-1312	28
β-strand	1319-1323	5	8
β-strand	1332-1335	4	8
α-helix	1337-1343	7
α-helix	1355-1358	4
β-strand	1364	1	1
α-helix	1365-1376	12
β-strand	1381-1388	8	8
β-strand	1394-1405	12	8
β-strand	1411-1418	8	8
β-strand	1420-1421	2	8
α-helix	1427-1447	21
α-helix	1453-1455	3
α-helix	1459-1465	7
α-helix	1466-1468	3
α-helix	1471-1491	21
α-helix	1494-1503	10
α-helix	1507-1509	3
α-helix	1514-1517	4
α-helix	1520-1526	7
α-helix	1528-1536	9
α-helix	1546-1580	35
β-strand	1583-1584	2	9
β-strand	1597	1	10
β-strand	1603	1	10
β-strand	1606-1614	9	9
β-strand	1619-1626	8	9
β-strand	1629-1635	7	9
β-strand	1656-1658	3	9
β-strand	1663-1664	2	9
β-strand	1669	1	11
β-strand	1684-1686	3	11
β-strand	1691-1693	3	11
β-strand	1694-1696	3	9
α-helix	1699-1721	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cell division control protein 42 homolog	A, C	protein	190	Homo sapiens	P60953 (AlphaFold model)
Intersectin-1,NPH1-1,Intersectin-1	B, D	protein	502	Homo sapiens, Avena sativa	O49003 (AlphaFold model), Q15811 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5HZK_1 Cell division control protein 42 homolog (chains A, C)
GAMQTIKCVVVGDGAVGKTCLLISYTTNKFPSEYVPTVFDNYAVTVMIGGEPYTLGLFDT
AGQEDYDRLRPLSYPQTDVFLVCFSVVSPSSFENVKEKWVPEITHHCPKTPFLLVGTQID
LRDDPSTIEKLAKNKQKPITPETAEKLARDLKAVKYVECSALTQRGLKNVFDEAILAALE
PPETQPKRKS

Sequence of entity 2 (B, D), FASTA

>5HZK_2 Intersectin-1,NPH1-1,Intersectin-1 (chains B, D)
MLTPTERKRQGYIHELIVTEENYVNDLQLVTEIFQKPLMESELLTEKEVAMIFVNWKELI
MCNIKLLKALRVRKKMSGELATTLERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREE
ILGRNCRFLQGPETDRATVRKIRDAIDNQTEVTVQLINYTKSGKKFWNLFHLQPMRDQKG
DVQYFIGVQLDGTEHVRDAAEREGVMLIKKTAENIDEAAKELKMPVKMIGDILSAQLPHM
QPYIRFCSRQLNGAALIQQKTDEAPDFKEFVKRLAMDPRCKGMPLSSFILKPMQRVTRYP
LIIKNILENTPENHPDHSHLKHALEKAEELCSQVNEGVREKENSDRLEWIQAHVQCEGLS
EQLVFNSVTNCLGPRKFLHSGKLYKAKSNKELYGFLFNDFLLLTQITKPLGSSGTDKVFS
PKSNLQYKMYKTPIFLNEVLVKLPTDPSGDEPIFHISHIDRVYTLRAESINERTAWVQKI
KAASELYIETEKKKLEHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
FMN	Flavin mononucleotide	C17 H21 N4 O9 P	2
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2

Primary citation

Engineering extrinsic disorder to control protein activity in living cells. Dagliyan, O., Tarnawski, M., Chu, P.H. et al. Science (2016) 354:1441-1444. DOI 10.1126/science.aah3404 · PubMed

Other PDB entries of the same protein (UniProt P60953 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2NGR 1.9 Å, Transition state complex for GTP hydrolysis by CDC42: comparisons of the high resolution…
4JS0 1.9 Å, Complex of Cdc42 with the CRIB-PR domain of IRSp53
6SUP 2.0 Å, Crystal Structure of TcdB2-TccC3-Cdc42
3VHL 2.08 Å, Crystal structure of the DHR-2 domain of DOCK8 in complex with Cdc42 (T17N mutant)
1GRN 2.1 Å, Crystal structure of the CDC42/CDC42GAP/ALF3 complex.
1NF3 2.1 Å, Structure of Cdc42 in a complex with the GTPase-binding domain of the cell polarity…
2DFK 2.15 Å, Crystal structure of the CDC42-Collybistin II complex
2WM9 2.2 Å, Structure of the complex between DOCK9 and Cdc42.
2WMO 2.2 Å, Structure of the complex between DOCK9 and Cdc42.
1GZS 2.3 Å, Crystal structure of the complex between the gef domain of the salmonella typhimurium…
1KI1 2.3 Å, Guanine Nucleotide Exchange Region of Intersectin in Complex with Cdc42
3GCG 2.3 Å, crystal structure of MAP and CDC42 complex

Browse structure collections

About this viewer

MolViewer shows 5HZK directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.