6KL4: MavC-UBE2N-Ub

Crystal structure of MavC-UBE2N-Ub. Determined by X-ray diffraction at 2.85 Å resolution. Released 15 Apr 2020.

Method: X-ray diffraction
Resolution: 2.85 Å
Organisms: Legionella pneumophila, Homo sapiens
Chains: 3
Atoms: 4,779
Mol. weight: 68.83 kDa
Released: 15 Apr 2020

Explore 6KL4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6KL4 contains 31 α-helices and 27 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: 21 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	11-24	14
α-helix	25-29	5
α-helix	33-44	12
α-helix	45-47	3
α-helix	54-64	11
α-helix	70-71	2
α-helix	74-85	12
α-helix	88-95	8
β-strand	100-101	2	1
α-helix	102-103	2
α-helix	107-111	5
β-strand	118-127	10	1
β-strand	132-135	4	2
β-strand	150-154	5	2
β-strand	157-161	5	2
β-strand	167-169	3	2
α-helix	174-183	10
α-helix	187-189	3
β-strand	191-193	3	2
α-helix	205-221	17
β-strand	227-237	11	1
β-strand	249-252	4	1
β-strand	254	1	3
β-strand	258	1	3
α-helix	260-265	6
α-helix	268-273	6
α-helix	277-287	11
α-helix	293-304	12
α-helix	306	1
α-helix	316-318	3
β-strand	324-329	6	1
β-strand	332	1	1
α-helix	335-352	18
α-helix	358-380	23

Chain B: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	6-17	12
α-helix	19-20	2
β-strand	23-27	5	4
β-strand	34-40	7	4
β-strand	51-57	7	4
α-helix	62-64	3
α-helix	66-67	2
β-strand	68-71	4	4
β-strand	80	1	5
β-strand	85	1	4
β-strand	86	1	5
α-helix	101-113	13
α-helix	123-131	9
α-helix	133-147	15

Chain C: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	6
β-strand	13-16	4	6
β-strand	22	1	7
α-helix	23-34	12
α-helix	38-40	3
β-strand	42-45	4	6
β-strand	48-49	2	6
β-strand	55	1	7
α-helix	56-59	4
β-strand	66-70	5	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MavC	A	protein	378	Legionella pneumophila	Q5ZTL4 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 N	B	protein	152	Homo sapiens	P61088 (AlphaFold model)
Ub	C	protein	76	Homo sapiens

Sequence of entity 1 (A), FASTA

>6KL4_1 MavC (chains A)
EKTGLHVHEKIKHMVKNYGTMITGIPAEILGQNEAEISVGYVKKMGNMKENIAEVVRKSE
MTQPTNSCGKASNEVCDLLLGTEGASEFEKSSYQVLSGDGSNLKGSLPNKNLLVRVEMDR
FNAPQKYQKIKREEFNPETAEKNKIYLLEDQLVYLDIFGKVIDLGQTSDTCHRLFNAITT
PFYQNYILYDEYIDPEESAEEAAMFEMGEIVKAKMKNIDCWTATHSFTIFVPESDSEDTR
TLYPYQAYWTSHTLQQWFSGDKDEKLSRLGIDGYIEKLALLGTTTDSKIRSSIYGELFSP
PGKEHVFCTGMNEKFSPLRVKFKVTEVNPEIALQNLEEVQEFIDTNYPGENAKDQCELYK
IKAQEAMTKQLEMRLLIE

Sequence of entity 2 (B), FASTA

>6KL4_2 Ubiquitin-conjugating enzyme E2 N (chains B)
MAGLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFLPE
EYPMAAPKVRFMTKIYHPNVDKLGRICLDILKDAWSPALQIRTVLLSIQALLSAPNPDDP
LANDVAEQWKTNEAQAIETARAWTRLYAMNNI

Sequence of entity 3 (C), FASTA

>6KL4_3 Ub (chains C)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Primary citation

Molecular Basis of Ubiquitination Catalyzed by the Bacterial Transglutaminase MavC. Guan, H., Fu, J., Yu, T. et al. Adv Sci (Weinh) (2020) 7:2000871-2000871. DOI 10.1002/advs.202000871 · PubMed

Other PDB entries of the same protein (UniProt Q5ZTL4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6P5H 1.53 Å, Structure of MavC middle insertion domain
6ULH 1.97 Å, Structure of MavC in complex with its substrate in R3 spacegroup
6K3B 1.97 Å, Crystal structure of Lpg2147-Lpg2149 complex
5TSC 2.01 Å, The crystal structure of Lpg2147 from Legionella pneumophila
6P5B 2.1 Å, Crystal Structure of MavC in Complex with Ub-UbE2N
6UMS 2.34 Å, Crystal structure of MavC in complex with its substrate mimic in C222(1) space group
6KG6 2.39 Å, Crystal structure of MavC/UBE2N-Ub complex
7BXH 2.7 Å, MavC-Lpg2149 complex
7BXG 2.71 Å, MavC-UBE2N-Ub complex
6UMP 2.8 Å, Crystal structure of MavC in complex with substrate mimic in P65 space group
6KFP 2.92 Å, Crystal structure of MavC ternary complex

Browse structure collections

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