6BG3: Endolysin, DCN1-like protein 1 chimera

Structure of (3S,4S)-1-benzyl-4-(3-(3-(trifluoromethyl)phenyl)ureido)piperidin-3-yl acetate bound to DCN1. Determined by X-ray diffraction at 1.05 Å resolution. Released 26 Sept 2018.

Method: X-ray diffraction
Resolution: 1.05 Å
Organisms: Enterobacteria phage T4, Homo sapiens
Chains: 1
Atoms: 3,711
Mol. weight: 44.74 kDa
Ligands: DOJ
Released: 26 Sept 2018

Explore 6BG3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6BG3 contains 20 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: 20 helices, 11 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	31-34	4	1
α-helix	39-50	12
β-strand	57	1	2
α-helix	60-79	20
α-helix	84-90	7
α-helix	93-112	20
α-helix	115-122	8
α-helix	126-134	9
α-helix	137-141	5
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	1153-1165	13
β-strand	1173-1174	2	4
α-helix	1175-1186	12
α-helix	1193-1202	10
β-strand	1207-1208	2	4
α-helix	1210-1222	13
α-helix	1238-1247	10

Molecules and chains

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

Sequence of entity 1 (A), FASTA

>6BG3_1 Endolysin, DCN1-like protein 1 chimera (chains A)
MGSSHHHHHHSQDLENLYFQGSMNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPS
LNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAA
LINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRTKRVITTFRTGTW
DAYKNLRKKLEQLYNRYKDPQDENKIGIDGIQQFCDDLALDPASISVLIIAWKFRAATQC
EFSKQEFMDGMTELGCDSIEKLKAQIPKMEQELKEPGRFKDFYQFTFNFAKNPGQKGLDL
EMAIAYWNLVLNGRFKFLDLWNKFLLEHHKRSIPKDTWNLLLDFSTMIADDMSNYDEEGA
WPVLIDDFVEFARPQIAGTKSTTV

Ligands and cofactors

ID	Name	Formula	Copies
DOJ	N-{(3S,4S)-1-benzyl-3-[(1S)-1-hydroxyethoxy]piperidin-4-yl}-N'-[3-(trifluoromet…	C22 H26 F3 N3 O3	1

Primary citation

Piperidinyl Ureas Chemically Control Defective in Cullin Neddylation 1 (DCN1)-Mediated Cullin Neddylation. Hammill, J.T., Scott, D.C., Min, J. et al. J Med Chem (2018) 61:2680-2693. DOI 10.1021/acs.jmedchem.7b01277 · 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
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…
1SX2 1.06 Å, Use of a Halide Binding Site to Bypass the 1000-atom Limit to Structure Determination by…

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