4GAO: DCN1-like protein 2

DCNL complex with N-terminally acetylated NEDD8 E2 peptide. Determined by X-ray diffraction at 3.28 Å resolution. Released 28 Nov 2012.

Method: X-ray diffraction
Resolution: 3.28 Å
Organism: Homo sapiens
Chains: 8
Atoms: 6,299
Mol. weight: 99.14 kDa
Released: 28 Nov 2012

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

Secondary structure: helices and β-sheets

4GAO contains 57 α-helices and 22 β-strands across 8 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: 13 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	62-70	9
β-strand	73-74	2	1
β-strand	77-81	5	1
α-helix	83-92	10
α-helix	100-109	10
β-strand	117-118	2	1
α-helix	119-128	10
α-helix	134-146	13
α-helix	147-149	3
α-helix	151-165	15
α-helix	167	1
β-strand	173-174	2	2
α-helix	175-185	11
α-helix	193-202	10
β-strand	207-208	2	2
α-helix	210-222	13
α-helix	238-247	10
α-helix	249-251	3

Chain B: 14 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	61-70	10
β-strand	74	1	3
β-strand	77	1	3
β-strand	80-81	2	4
α-helix	83-93	11
α-helix	100-109	10
β-strand	117-118	2	4
α-helix	119-128	10
α-helix	134-146	13
α-helix	147-149	3
α-helix	151-165	15
α-helix	167	1
β-strand	173	1	5
α-helix	175-185	11
α-helix	193-203	11
α-helix	207	1
β-strand	208	1	5
α-helix	209	1
α-helix	210-222	13
α-helix	238-250	13

Chains C, E, F and H: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	4-9	6

Chain D: 11 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	63-70	8
β-strand	74	1	6
β-strand	77	1	6
β-strand	80-81	2	7
α-helix	83-92	10
α-helix	100-109	10
β-strand	117-118	2	7
α-helix	119-129	11
α-helix	134-146	13
α-helix	151-165	15
α-helix	167	1
β-strand	173-174	2	8
α-helix	175-185	11
α-helix	193-202	10
β-strand	207-208	2	8
α-helix	210-222	13
α-helix	238-247	10

Chain G: 15 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	61-72	12
β-strand	73-74	2	9
β-strand	77-81	5	9
α-helix	83-92	10
α-helix	100-109	10
β-strand	117-118	2	9
α-helix	119-129	11
α-helix	134-145	12
α-helix	146-149	4
α-helix	151-165	15
α-helix	167	1
β-strand	173	1	10
α-helix	175-185	11
α-helix	193-203	11
α-helix	207	1
β-strand	208	1	10
α-helix	209	1
α-helix	210-222	13
α-helix	238-247	10
α-helix	248-250	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DCN1-like protein 2	A, B, D, G	protein	200	Homo sapiens	Q6PH85 (AlphaFold model)
NEDD8-conjugating enzyme Ubc12	C, E, F, H	protein	12	Homo sapiens	P61081 (AlphaFold model)

Sequence of entity 1 (A, B, D, G), FASTA

>4GAO_1 DCN1-like protein 2 (chains A, B, D, G)
GSKKKLERLYGRYKDPQDENKIGVDGIQQFCDDLSLDPASISVLVIAWKFRAATQCEFSR
KEFLDGMTELGCDSMEKLKALLPRLEQELKDTAKFKDFYQFTFTFAKNPGQKGLDLEMAV
AYWKLVLSGRFKFLDLWNTFLMEHHKRSIPRDTWNLLLDFGNMIADDMSNYDEEGAWPVL
IDDFVEYARPVVTGGKRSLF

Sequence of entity 2 (C, E, F, H), FASTA

>4GAO_2 NEDD8-conjugating enzyme Ubc12 (chains C, E, F, H)
MIKLFSLKQQKK

Primary citation

Structural Conservation of Distinctive N-terminal Acetylation-Dependent Interactions across a Family of Mammalian NEDD8 Ligation Enzymes. Monda, J.K., Scott, D.C., Miller, D.J. et al. Structure (2013) 21:42-53. DOI 10.1016/j.str.2012.10.013 · PubMed

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