5V83: DCN1

Name: PDB 5V83: Structure of DCN1 bound to NAcM-HIT
Published: 2017-05-24
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Structure of DCN1 bound to NAcM-HIT. Determined by X-ray diffraction at 2.0 Å resolution. Released 24 May 2017.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: Enterobacteria phage T4, Homo sapiens
Chains: 1
Atoms: 3,245
Mol. weight: 44.68 kDa
Ligands: 8Z7
Released: 24 May 2017

Explore 5V83 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5V83 contains 21 α-helices and 12 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: 21 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	-8--5	4
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	31-32	2	1
α-helix	39-50	12
β-strand	57	1	2
α-helix	60-80	21
α-helix	85-90	6
α-helix	93-112	20
α-helix	115-122	8
α-helix	126-133	8
α-helix	137-141	5
α-helix	143-155	13
α-helix	159-1070	15
β-strand	1074	1	3
β-strand	1077	1	3
β-strand	1080-1081	2	4
α-helix	1083-1092	10
α-helix	1100-1108	9
β-strand	1117-1118	2	4
α-helix	1119-1129	11
α-helix	1134-1147	14
α-helix	1151-1165	15
β-strand	1173	1	5
α-helix	1175-1185	11
α-helix	1193-1202	10
α-helix	1204-1205	2
β-strand	1208	1	5
α-helix	1210-1222	13
α-helix	1238-1251	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lysozyme,DCN1-like protein 1 chimera	A	protein	384	Enterobacteria phage T4, Homo sapiens	P00720, Q96GG9 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5V83_1 Lysozyme,DCN1-like protein 1 chimera (chains A)
MGSSHHHHHHSQDLENLYFQGSMNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPS
LNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAA
LINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRTKRVITTFRTGTW
DAYKNLRKKLEQLYNRYKDPQDENKIGIDGIQQFCDDLALDPASISVLIIAWKFRAATQC
EFSKQEFMDGMTELGCDSIEKLKAQIPKMEQELKEPGRFKDFYQFTFNFAKNPGQKGLDL
EMAIAYWNLVLNGRFKFLDLWNKFLLEHHKRSIPKDTWNLLLDFSTMIADDMSNYDEEGA
WPVLIDDFVEFARPQIAGTKSTTV

Ligands and cofactors

ID	Name	Formula	Copies
8Z7	N-(1-benzylpiperidin-4-yl)-N'-[3-(trifluoromethyl)phenyl]urea	C20 H22 F3 N3 O	1

Primary citation

Blocking an N-terminal acetylation-dependent protein interaction inhibits an E3 ligase. Scott, D.C., Hammill, J.T., Min, J. et al. Nat Chem Biol (2017) 13:850-857. DOI 10.1038/nchembio.2386 · PubMed

Other PDB entries of the same protein (UniProt P00720), best resolution first:

2O7A 0.84 Å, T4 lysozyme C-terminal fragment
5JDT 1.0 Å, Structure of Spin-labelled T4 lysozyme mutant L118C-R1 at 100K
7LOE 1.01 Å, T4 lysozyme mutant L99A in complex with 1-fluoranylnaphthalene
7LOD 1.02 Å, T4 lysozyme mutant L99A in complex with 1-fluoranyl-4-iodanyl-benzene
7LX8 1.03 Å, T4 lysozyme mutant L99A
5XPF 1.04 Å, High-resolution X-ray structure of the T26H mutant of T4 lysozyme
6BG3 1.05 Å, Structure of (3S,4S)-1-benzyl-4-(3-(3-(trifluoromethyl)phenyl)ureido)piperidin-3-yl…
7LOF 1.05 Å, T4 lysozyme mutant L99A in complex with 2-butylthiophene
7LX6 1.05 Å, T4 lysozyme mutant L99A
7LX7 1.05 Å, T4 lysozyme mutant L99A
1SWY 1.06 Å, Use of a Halide Binding Site to Bypass the 1000-atom Limit to Ab initio Structure…
1SWZ 1.06 Å, Use of an ion-binding site to bypass the 1000-atom limit to ab initio structure…

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