6Z2Q: Wild type OgpA from Akkermansia muciniphila

Crystal structure of wild type OgpA from Akkermansia muciniphila in complex with an O-glycopeptide (GalGalNAc-TS) product. Determined by X-ray diffraction at 2.35 Å resolution. Released 30 Sept 2020.

Method: X-ray diffraction
Resolution: 2.35 Å
Organisms: Akkermansia muciniphila ATCC BAA-835, synthetic construct
Chains: 2
Atoms: 2,928
Mol. weight: 44.76 kDa
Ligands: ZN
Released: 30 Sept 2020

Explore 6Z2Q in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6Z2Q contains 15 α-helices and 20 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: 15 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	30-32	3
β-strand	44-45	2	1
β-strand	46-51	6	2
α-helix	56-58	3
α-helix	61-82	22
β-strand	91-92	2	1
β-strand	94-96	3	3
β-strand	99-100	2	3
β-strand	103-106	4	2
α-helix	111-113	3
α-helix	120-133	14
α-helix	136-138	3
β-strand	144-149	6	2
α-helix	150-151	2
β-strand	157	1	4
β-strand	160	1	4
β-strand	167-169	3	2
β-strand	172-177	6	2
α-helix	183-185	3
α-helix	191-210	20
β-strand	217	1	5
α-helix	220-226	7
β-strand	228-229	2	6
α-helix	234-236	3
β-strand	243-244	2	6
α-helix	247-254	8
α-helix	257-259	3
β-strand	275-284	10	5
β-strand	287-308	22	5
β-strand	321-339	19	5
α-helix	340-342	3
β-strand	350-359	10	5
β-strand	364-372	9	5
α-helix	373-375	3
β-strand	379-380	2	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
O-glycan protease	A	protein	371	Akkermansia muciniphila ATCC BAA-835	B2UR60 (AlphaFold model)
Glycodrosocin	D	protein	19	synthetic construct	P36193 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6Z2Q_1 O-glycan protease (chains A)
MEVTVPDALKDRIALKKTARQLNIVYFLGSDTEPVPDYERRLSELLLYLQQFYGKEMQRH
GYGARSFGLDIKSPGRVNIIEYKAKNPAAHYPYENGGGWKAAQELDEFFKAHPDRKKSQH
TLIIMPTWNDEKNGPDNPGGVPFYGMGRNCFALDYPAFDIKHLGQKTREGRLLTKWYGGM
AHELGHGLNLPHNHQTASDGKKYGTALMGSGNYTFGTSPTFLTPASCALLDACEVFSVTP
SQQFYEGKPEVEVGDVAISFKGDQILVSGNYKSPQTVKALNVYIQDPPYAVNQDYDAVSF
SRRLGKKSGKFSMKIDKKELEGLNNNEFRISLMFILANGLHMQKHFTFHWDALQDYRDGS
KSGSGHHHHHH

Sequence of entity 2 (D), FASTA

>6Z2Q_2 Glycodrosocin (chains D)
GKPRPYSPRPTSHPRPIRV

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Water and common crystallization additives (EDO, ACY) are not listed.

Primary citation

Structural basis of mammalian mucin processing by the human gut O-glycopeptidase OgpA from Akkermansia muciniphila. Trastoy, B., Naegeli, A., Anso, I. et al. Nat Commun (2020) 11:4844-4844. DOI 10.1038/s41467-020-18696-y · PubMed

Other PDB entries of the same protein (UniProt B2UR60 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6Z2O 1.65 Å, Crystal structure of wild type OgpA from Akkermansia muciniphila in P 21 21 21
6Z2D 1.9 Å, Crystal structure of wild type OgpA from Akkermansia muciniphila in P 41 21 2
6Z2P 2.16 Å, Crystal structure of catalytic inactive OgpA from Akkermansia muciniphila in complex…

Browse structure collections

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