5YM9: Deamidase from Legionella pneumophila

Crystal Structure of the Deamidase from Legionella pneumophila. Determined by X-ray diffraction at 2.5 Å resolution. Released 24 Oct 2018.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)
Chains: 2
Atoms: 6,405
Mol. weight: 88.09 kDa
Released: 24 Oct 2018

Explore 5YM9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5YM9 contains 50 α-helices and 24 β-strands across 2 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: 25 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	16-31	16
α-helix	32-36	5
α-helix	40-51	12
α-helix	52-54	3
α-helix	61-75	15
α-helix	83-95	13
α-helix	97-105	9
α-helix	107-108	2
β-strand	109-110	2	1
α-helix	111-112	2
α-helix	116-123	8
β-strand	132-141	10	1
β-strand	146-149	4	2
α-helix	152-154	3
α-helix	161	1
β-strand	164-167	4	2
β-strand	172-175	4	2
β-strand	181-183	3	2
α-helix	188-197	10
β-strand	203-205	3	2
α-helix	218-232	15
α-helix	234-236	3
β-strand	240-250	11	1
α-helix	251-253	3
α-helix	257-259	3
β-strand	262-264	3	1
β-strand	267	1	3
β-strand	271	1	3
α-helix	273-278	6
α-helix	281-286	6
α-helix	290-302	13
α-helix	306-317	12
α-helix	319	1
α-helix	329-331	3
β-strand	337-345	9	1
α-helix	348-363	16
α-helix	370-393	24

Chain B: 25 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	16-31	16
α-helix	32-36	5
α-helix	40-51	12
α-helix	52-54	3
α-helix	61-76	16
α-helix	83-95	13
α-helix	97-105	9
α-helix	107-108	2
β-strand	109-110	2	4
α-helix	111-112	2
α-helix	116-123	8
β-strand	132-141	10	4
β-strand	146-149	4	5
α-helix	152-154	3
α-helix	161	1
β-strand	164-167	4	5
β-strand	172-175	4	5
β-strand	181-183	3	5
α-helix	188-197	10
β-strand	203-205	3	5
α-helix	209-212	4
α-helix	218-232	15
α-helix	234-236	3
β-strand	240-250	11	4
α-helix	251-253	3
α-helix	257-259	3
β-strand	262-264	3	4
β-strand	267	1	6
β-strand	271	1	6
α-helix	273-278	6
α-helix	281-286	6
α-helix	290-302	13
α-helix	306-317	12
α-helix	319	1
β-strand	337-345	9	4
α-helix	348-363	16
α-helix	370-393	24

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Uncharacterized protein	A, B	protein	384	Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)	Q5ZTL3 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5YM9_1 Uncharacterized protein (chains A, B)
KLESPGFMVHKKLKSMSQSYGVMMTGVPAEVLGQMQAERSIPSINKTGNLKQQIAKEVSK
VCHMMTEPTQSCGQASNDVCELLLGKIEAEKFHFTKYEALSADGDNLKNVLENTAPSSTN
LLIRFEIDREDPPIVLVKTKNENFNPETAVKNKIYLLENKLYFIDKMGNLFNLGPGKKKC
TQLFNAIGDSAEYSLCDPFVLEEPEKPEDFAISEIVDIFNEQKERFDFWIGSHSFTIYIP
QTLGESPRQFYPYQAYFGSHTLQDWFVSDKDEYLSRIGIDKYIEKLAVLGKTTNTKERSD
IYAEFFSKRGREAFFCAHLNEKRQPLRVKFKITEINPELALKNLQETQEFIDTHPGENPS
DKVENYRNRAKLAMTEHLESLLDI

Primary citation

Crystal Structure of the Deamidase from Legionella pneumophila. Zhu, Z.L., Zhu, M. To be published.

Other PDB entries of the same protein (UniProt Q5ZTL3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6K11 1.94 Å, Crystal structure of MvcA from Legionella pneumophila
5SUJ 2.36 Å, Crystal structure of uncharacterized protein LPG2148 from Legionella pneumophila
6JKY 2.45 Å, Crystal structure of MvcA-UBE2N-Ub complex from Legionella pneumophila
6LP2 2.48 Å, Structure of Lpg2148/UBE2N-Ub complex
6LW4 2.7 Å, Structure of Lpg2148/Lpg2149 complex
7BXF 2.7 Å, MvcA-Lpg2149 complex

Browse structure collections

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