6XOM: DCN1

DCN1 bound to 8. Determined by X-ray diffraction at 2.1 Å resolution. Released 2 Jun 2021.

Method: X-ray diffraction
Resolution: 2.1 Å
Organisms: Enterobacteria phage T4, Homo sapiens
Chains: 1
Atoms: 3,137
Mol. weight: 45.02 kDa
Ligands: H8V
Released: 2 Jun 2021

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

Secondary structure: helices and β-sheets

6XOM contains 22 α-helices and 11 β-strands across 1 chain. 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: 22 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	3-10	8
β-strand	14-15	2	1
β-strand	16	1	2
β-strand	17-19	3	1
β-strand	25-28	4	1
β-strand	31-34	4	1
α-helix	39-50	12
β-strand	57	1	2
α-helix	60-79	20
α-helix	85-90	6
α-helix	93-112	20
α-helix	115-122	8
α-helix	126-133	8
α-helix	138-141	4
α-helix	143-155	13
α-helix	159-1072	17
β-strand	1073-1074	2	3
β-strand	1077-1081	5	3
α-helix	1083-1092	10
α-helix	1100-1108	9
β-strand	1117-1118	2	3
α-helix	1119-1128	10
α-helix	1134-1147	14
α-helix	1151-1165	15
α-helix	1167	1
β-strand	1173	1	4
α-helix	1175-1185	11
α-helix	1193-1199	7
α-helix	1200-1204	5
β-strand	1208	1	4
α-helix	1210-1222	13
α-helix	1238-1247	10
α-helix	1248-1250	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lysozyme, DCN1-like protein 1 chimera	A	protein	386	Enterobacteria phage T4, Homo sapiens	D9IEF7, Q96GG9 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6XOM_1 Lysozyme, DCN1-like protein 1 chimera (chains A)
MHHHHHHSSGVDLGTENLYFQSNAMNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKS
PSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRR
AALINMVFQMGETGVAGFTNSLRMLQQKRWAEAAVNLAKSRWYNQTPNRTKRVITTFATG
TWDAYKNLRKKLEQLYNRYKDPQDENKIGIDGIQQFCDDLALDPASISVLIIAWKFRAAT
QCEFSKQEFMDGMTELGCDSIEKLKAQIPKMEQELKEPGRFKDFYQFTFNFAKNPGQKGL
DLEMAIAYWNLVLNGRFKFLDLWNKFLLEHHKRSIPKDTWNLLLDFSTMIADDMSNYDEE
GAWPVLIDDFVEFARPQIAGTKSTTV

Ligands and cofactors

ID	Name	Formula	Copies
H8V	(2R)-N-[(2S)-2-cyclohexyl-2-({N-propanoyl-3-[6-(propan-2-yl)-1,3-benzothiazol-2…	C33 H51 N5 O4 S	1

Water and common crystallization additives (EDO) are not listed.

Primary citation

Selective inhibition of cullin 3 neddylation through covalent targeting DCN1 protects mice from acetaminophen-induced liver toxicity. Zhou, H., Lu, J., Chinnaswamy, K. et al. Nat Commun (2021) 12:2621-2621. DOI 10.1038/s41467-021-22924-4 · PubMed

Other PDB entries of the same protein (UniProt D9IEF7), best resolution first:

7LOG 0.99 Å, T4 lysozyme mutant L99A in complex with 3-butylpyridine
9DJK 1.04 Å, T4 Lysozyme D127H/V131H
7XE7 1.05 Å, T4 lysozyme mutant-S44C/C54T/N68C/A93C/C97A/T115C, pH10
7LXA 1.07 Å, T4 lysozyme mutant L99A
9DJM 1.08 Å, T4 Lysozyme K147H/T151H
7XE6 1.1 Å, T4 lysozyme mutant-S44C/C54T/N68C/A93C/C97A/T115C, pH7
7XEA 1.1 Å, T4 lysozyme mutant-S44C/C54T/N68C/A93C/C97A/T115C, DMSO 40%, and then backsoaking
9DJI 1.1 Å, T4 Lysozyme R119H/Q123H
9DJD 1.11 Å, T4 Lysozyme A73H/G77H/Y139F co-crystallized with Cu(II)-NTA
8F11 1.12 Å, T4 lysozyme with a 2,6-diazaadamantane nitroxide (DZD) spin label
9DJB 1.13 Å, T4 Lysozyme A73H/G77H
9DJC 1.13 Å, T4 Lysozyme A73H/G77H/Y139F

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