6B5Q: DCN1

DCN1 bound to 38. Determined by X-ray diffraction at 2.16 Å resolution. Released 28 Feb 2018.

Method: X-ray diffraction
Resolution: 2.16 Å
Organisms: Homo sapiens, synthetic construct
Chains: 4
Atoms: 3,249
Mol. weight: 54.25 kDa
Released: 28 Feb 2018

Explore 6B5Q in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6B5Q contains 22 α-helices and 10 β-strands across 2 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: 11 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	63-70	8
β-strand	73	1	1
β-strand	80-81	2	1
α-helix	83-92	10
α-helix	100-108	9
β-strand	117-118	2	1
α-helix	119-128	10
α-helix	134-147	14
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

Chain B: 11 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	63-70	8
β-strand	73	1	3
β-strand	81	1	3
α-helix	83-92	10
α-helix	100-108	9
β-strand	117	1	3
α-helix	119-128	10
α-helix	134-139	6
α-helix	141-147	7
α-helix	153-165	13
β-strand	173-174	2	4
α-helix	175-185	11
α-helix	193-200	8
β-strand	207-208	2	4
α-helix	210-222	13
α-helix	238-247	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DCN1-like protein 1	A, B	protein	225	Homo sapiens	Q96GG9 (AlphaFold model)
Peptidomimetic Inhibitors DI-591	D, E	protein	5	synthetic construct

Sequence of entity 1 (A, B), FASTA

>6B5Q_1 DCN1-like protein 1 (chains A, B)
MSYYHHHHHHLESTSLYKKAGTMGSLDRKKLEQLYNRYKDPQDENKIGIDGIQQFCDDLA
LDPASISVLIIAWKFRAATQCEFSKQEFMDGMTELGCDSIEKLKAQIPKMEQELKEPGRF
KDFYQFTFNFAKNPGQKGLDLEMAIAYWNLVLNGRFKFLDLWNKFLLEHHKRSIPKDTWN
LLLDFSTMIADDMSNYDEEGAWPVLIDDFVEFARPQIAGTKSTTV

Sequence of entity 2 (D, E), FASTA

>6B5Q_2 Peptidomimetic Inhibitors DI-591 (chains D, E)
XXXKX

Primary citation

High-Affinity Peptidomimetic Inhibitors of the DCN1-UBC12 Protein-Protein Interaction. Zhou, H., Zhou, W., Zhou, B. et al. J Med Chem (2018) 61:1934-1950. DOI 10.1021/acs.jmedchem.7b01455 · PubMed

Other PDB entries of the same protein (UniProt Q96GG9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6BG3 1.05 Å, Structure of (3S,4S)-1-benzyl-4-(3-(3-(trifluoromethyl)phenyl)ureido)piperidin-3-yl…
6BG5 1.1 Å, Structure of 1-(benzo[d][1,3]dioxol-5-ylmethyl)-1-(1-propylpiperidin-4-yl)-3-(3-(trifluor…
5V86 1.37 Å, Structure of DCN1 bound to NAcM-OPT
6P5V 1.4 Å, Structure of DCN1 bound to N-((4S,5S)-7-ethyl-4-(4-fluorophenyl)-3-methyl-6-oxo-1-phenyl-…
3TDU 1.5 Å, N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein…
7KWA 1.57 Å, Structure of DCN1 bound to N-((4S,5S)-3-(aminomethyl)-7-ethyl-4-(4-fluorophenyl)-6-oxo-1-…
5V88 1.6 Å, Structure of DCN1 bound to NAcM-COV
6P5W 1.69 Å, Structure of DCN1 bound to 3-methyl-N-((4S,5S)-3-methyl-6-oxo-1-phenyl-4-(p-tolyl)-4,5,6,…
3TDZ 2.0 Å, N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein…
5V83 2.0 Å, Structure of DCN1 bound to NAcM-HIT
6XOO 2.06 Å, DCN1 bound to DI-1859
6XOP 2.07 Å, DCN1 bound to inhibitor 10

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