Crystal structure of catalytic inactive OgpA from Akkermansia muciniphila in complex with an O-glycopeptide (glycodrosocin) substrate. Determined by X-ray diffraction at 2.16 Å resolution. Released 30 Sept 2020.
Explore 6Z2P in 3D Show helices and sheets RCSB PDB PDBe
6Z2P contains 19 α-helices and 21 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.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 27-29 | 3 | |
| 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 | 120-134 | 15 | |
| 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 | 247-253 | 7 | |
| α-helix | 257-259 | 3 | |
| β-strand | 275-284 | 10 | 5 |
| β-strand | 287-308 | 22 | 5 |
| α-helix | 309 | 1 | |
| α-helix | 311 | 1 | |
| 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 | 1 | 5 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 6-7 | 2 | 2 |
| α-helix | 8-9 | 2 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| O-glycan protease | A | protein | 371 | Akkermansia muciniphila ATCC BAA-835 | B2UR60 (AlphaFold model) |
| Glycodrosocin | C | protein | 19 | synthetic construct | P36193 (AlphaFold model) |
>6Z2P_1 O-glycan protease (chains A) MEVTVPDALKDRIALKKTARQLNIVYFLGSDTEPVPDYERRLSELLLYLQQFYGKEMQRH GYGARSFGLDIKSPGRVNIIEYKAKNPAAHYPYENGGGWKAAQELDEFFKAHPDRKKSQH TLIIMPTWNDEKNGPDNPGGVPFYGMGRNCFALDYPAFDIKHLGQKTREGRLLTKWYGGM AAALGHGLNLPHNHQTASDGKKYGTALMGSGNYTFGTSPTFLTPASCALLDACEVFSVTP SQQFYEGKPEVEVGDVAISFKGDQILVSGNYKSPQTVKALNVYIQDPPYAVNQDYDAVSF SRRLGKKSGKFSMKIDKKELEGLNNNEFRISLMFILANGLHMQKHFTFHWDALQDYRDGS KSGSGHHHHHH
>6Z2P_2 Glycodrosocin (chains C) GKPRPYSPRPTSHPRPIRV
| ID | Name | Formula | Copies |
|---|---|---|---|
| CA | Calcium ion | Ca | 1 |
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:
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