6CP2: SidC

SidC in complex with UbcH7~Ub. Determined by X-ray diffraction at 2.9 Å resolution. Released 1 Aug 2018.

Method: X-ray diffraction
Resolution: 2.9 Å
Organisms: Legionella pneumophila, Homo sapiens
Chains: 3
Atoms: 5,957
Mol. weight: 88.88 kDa
Released: 1 Aug 2018

Explore 6CP2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6CP2 contains 32 α-helices and 38 β-strands across 3 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: 23 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	20-22	3	1
β-strand	28-30	3	1
β-strand	31-36	6	2
β-strand	37	1	3
β-strand	40	1	4
β-strand	41	1	3
β-strand	43-44	2	5
α-helix	45-47	3
α-helix	50-57	8
β-strand	59-61	3	6
β-strand	64-66	3	6
α-helix	69-88	20
α-helix	101-124	24
α-helix	141-144	4
α-helix	145-152	8
β-strand	157-161	5	4
β-strand	178	1	4
β-strand	184	1	7
α-helix	186-188	3
β-strand	196	1	7
α-helix	202-210	9
β-strand	218-219	2	8
α-helix	225-234	10
α-helix	248-268	21
α-helix	272-276	5
β-strand	281	1	9
β-strand	287	1	9
α-helix	290-291	2
α-helix	292-296	5
α-helix	306-317	12
α-helix	321-325	5
β-strand	337-338	2	8
α-helix	341-364	24
α-helix	372-377	6
α-helix	381-395	15
α-helix	400-408	9
α-helix	419-421	3
α-helix	422-438	17
β-strand	447-451	5	4
β-strand	460-462	3	2
β-strand	465-469	5	2
α-helix	470-477	8
α-helix	490-496	7
β-strand	501-502	2	2

Chain B: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	2-16	15
β-strand	22-27	6	10
β-strand	34-39	6	10
β-strand	50	1	11
β-strand	51-56	6	10
β-strand	67-70	4	10
β-strand	79	1	12
β-strand	84	1	10
β-strand	85	1	12
α-helix	88-90	3
α-helix	101-113	13
α-helix	123-130	8
α-helix	133-147	15
β-strand	149	1	11
α-helix	150-151	2

Chain C: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	1-7	7	13
β-strand	13-17	5	13
β-strand	22	1	14
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	13
β-strand	48-49	2	13
α-helix	50-51	2
β-strand	55	1	14
β-strand	66-71	6	13
β-strand	74-75	2	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
SidC	A	protein	542	Legionella pneumophila	Q6RCR4 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 L3	B	protein	154	Homo sapiens	P68036 (AlphaFold model)
Polyubiquitin-B	C	protein	78	Homo sapiens	P0CG47 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6CP2_1 SidC (chains A)
MVINMVDVIKFKEPERCDYLYVDENNKVHILLPIVGGDEIGLDNTAQTAVELITFFYGSA
HSGVTKYSAEHQLSEYKRQLEEDIKAINSQKKISPHAYDDLLKEKIERLQQIEKYIELIQ
VLKKQYDEQNDIRQLRTGGIPQLPSGVKEIIKSSENAFAVRLSPYDNDKFTRFDDPLFNV
KRNISKYDTPSRQAPIPIYEGLGYRLRSTLFPEDKTPTPINKKSLRDKVKSTVLSHYKDE
DRIDGEKKDEKLNELITNLQNELVKELVKSDPQYSKLSLSKDPRGKEINYDYLVNSLMLV
DNDSEIGDWIDTILDATVDSTVWVAQASSPFYDGAKEISSDRDADKISIRVQYLLAEANI
YCKTNKLSDANFGEFFDKEPHATEIAKRVKEGFTQGADIEPIIYDYINSNHAELGLKSPL
TGKQQQEITDKFTKHYNTIKESPHFDEFFVADPDKKGNIFSHQGRISCHFLDFFTRQTKG
KHPLGDLASHQEALQEGTSNRLHHKNEVVAQGYEKLDQFKKEVVKLLAENKPKELLDYLV
AT

Sequence of entity 2 (B), FASTA

>6CP2_2 Ubiquitin-conjugating enzyme E2 L3 (chains B)
MAASRRLMKELEEIRKCGMKNFRNIQVDEANLLTWQGLIVPDNPPYDKGAFRIEINFPAE
YPFKPPKITFKTKIYHPNIDEKGQVKLPVISAENWKPATKTDQVIQSLIALVNDPQPEHP
LRADLAEEYSKDRKKFCKNAEEFTKKYGEKRPVD

Sequence of entity 3 (C), FASTA

>6CP2_3 Polyubiquitin-B (chains C)
GSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSD
YNIQKESTLHLVLRLRGG

Primary citation

Insights into the ubiquitin transfer cascade catalyzed by theLegionellaeffector SidC. Wasilko, D.J., Huang, Q., Mao, Y. Elife (2018) 7. DOI 10.7554/eLife.36154 · PubMed

Other PDB entries of the same protein (UniProt Q6RCR4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4TRH 2.03 Å, The Legionella effector SidC defines a unique family of ubiquitin ligases important for…
4TRG 2.59 Å, the SNL domain of SidC
4ZUZ 2.86 Å, SidC 1-871

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