Crystal structure of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase in complex with Mn, UDP and Mannosyl-peptide. Determined by X-ray diffraction at 2.6 Å resolution. Released 10 Aug 2016.
Explore 5GGI in 3D Show helices and sheets RCSB PDB PDBe
5GGI contains 56 α-helices and 47 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.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 260-269 | 10 | |
| α-helix | 276-278 | 3 | |
| α-helix | 284-286 | 3 | |
| α-helix | 291-293 | 3 | |
| β-strand | 304-308 | 5 | 1 |
| α-helix | 312-322 | 11 | |
| α-helix | 330-332 | 3 | |
| β-strand | 333-337 | 5 | 1 |
| α-helix | 342-351 | 10 | |
| β-strand | 354-357 | 4 | 1 |
| α-helix | 364-382 | 19 | |
| β-strand | 388-393 | 6 | 1 |
| β-strand | 396-398 | 3 | 2 |
| α-helix | 402-415 | 14 | |
| β-strand | 419-423 | 5 | 1 |
| β-strand | 430 | 1 | 3 |
| β-strand | 440-443 | 4 | 1 |
| β-strand | 451-454 | 4 | 1 |
| α-helix | 455-457 | 3 | |
| α-helix | 458-462 | 5 | |
| α-helix | 463-465 | 3 | |
| α-helix | 466-468 | 3 | |
| α-helix | 475-479 | 5 | |
| α-helix | 482-485 | 4 | |
| β-strand | 489-493 | 5 | 1 |
| β-strand | 496 | 1 | 4 |
| β-strand | 498-500 | 3 | 2 |
| α-helix | 510-516 | 7 | |
| β-strand | 520 | 1 | 3 |
| β-strand | 522 | 1 | 4 |
| α-helix | 528-530 | 3 | |
| α-helix | 533-536 | 4 | |
| α-helix | 538-551 | 14 | |
| α-helix | 552 | 1 | |
| β-strand | 553-554 | 2 | 5 |
| α-helix | 555 | 1 | |
| α-helix | 564-566 | 3 | |
| β-strand | 574-581 | 8 | 5 |
| α-helix | 588-597 | 10 | |
| β-strand | 611-616 | 6 | 5 |
| β-strand | 619-627 | 9 | 5 |
| α-helix | 630-634 | 5 | |
| α-helix | 639-641 | 3 | |
| β-strand | 642 | 1 | 5 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 98-105 | 8 | 6 |
| β-strand | 106 | 1 | 7 |
| β-strand | 110-114 | 5 | 6 |
| β-strand | 117-122 | 6 | 6 |
| β-strand | 130-136 | 7 | 7 |
| β-strand | 143-149 | 7 | 7 |
| α-helix | 156-165 | 10 | |
| α-helix | 168 | 1 | |
| β-strand | 172-178 | 7 | 7 |
| α-helix | 187-195 | 9 | |
| α-helix | 201-203 | 3 | |
| β-strand | 209-215 | 7 | 7 |
| β-strand | 220-226 | 7 | 7 |
| α-helix | 234-237 | 4 | |
| β-strand | 238-245 | 8 | 6 |
| α-helix | 260-269 | 10 | |
| α-helix | 276-278 | 3 | |
| α-helix | 284-286 | 3 | |
| α-helix | 291-293 | 3 | |
| β-strand | 304-308 | 5 | 8 |
| α-helix | 312-322 | 11 | |
| α-helix | 330-332 | 3 | |
| β-strand | 333-338 | 6 | 8 |
| α-helix | 342-350 | 9 | |
| β-strand | 354-358 | 5 | 8 |
| α-helix | 365-382 | 18 | |
| β-strand | 388-393 | 6 | 8 |
| β-strand | 396-398 | 3 | 9 |
| α-helix | 399 | 1 | |
| α-helix | 402-415 | 14 | |
| β-strand | 419-423 | 5 | 8 |
| β-strand | 430 | 1 | 10 |
| β-strand | 440-443 | 4 | 8 |
| β-strand | 451-454 | 4 | 8 |
| α-helix | 455-457 | 3 | |
| α-helix | 458-462 | 5 | |
| α-helix | 463-465 | 3 | |
| α-helix | 466-468 | 3 | |
| α-helix | 475-479 | 5 | |
| α-helix | 482-485 | 4 | |
| β-strand | 489-493 | 5 | 8 |
| β-strand | 498-500 | 3 | 9 |
| α-helix | 510-516 | 7 | |
| β-strand | 520 | 1 | 10 |
| α-helix | 528-530 | 3 | |
| α-helix | 533-536 | 4 | |
| α-helix | 538-551 | 14 | |
| α-helix | 552 | 1 | |
| β-strand | 553-554 | 2 | 11 |
| α-helix | 555 | 1 | |
| α-helix | 564-566 | 3 | |
| β-strand | 574-581 | 8 | 11 |
| α-helix | 588-596 | 9 | |
| β-strand | 607-608 | 2 | 11 |
| β-strand | 611-616 | 6 | 11 |
| β-strand | 619-627 | 9 | 11 |
| α-helix | 630-634 | 5 | |
| β-strand | 642 | 1 | 11 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 2-4 | 3 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1 | A, B | protein | 578 | Homo sapiens | Q8WZA1 (AlphaFold model) |
| mannosyl-peptide | F, G | protein | 11 | Homo sapiens |
>5GGI_1 Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1 (chains A, B) GSGPRRVLDVEVYSSRSKVYVAVDGTTVLEDEAREQGRGIHVIVLNQATGHVMAKRVFDT YSPHEDEAMVLFLNMVAPGRVLICTVKDEGSFHLKDTAKALLRSLGSQAGPALGWRDTWA FVGRKGGPVFGEKHSKSPALSSWGDPVLLKTDVPLSSAEEAECHWADTELNRRRRRFCSK VEGYGSVCSCKDPTPIEFSPDPLPDNKVLNVPVAVIAGNRPNYLYRMLRSLLSAQGVSPQ MITVFIDGYYEEPMDVVALFGLRGIQHTPISIKNARVSQHYKASLTATFNLFPEAKFAVV LEEDLDIAVDFFSFLSQSIHLLEEDDSLYCISAWNDQGYEHTAEDPALLYRVETMPGLGW VLRRSLYKEELEPKWPTPEKLWDWDMWMRMPEQRRGRECIIPDVSRSYHFGIVGLNMNGY FHEAYFKKHKFNTVPGVQLRNVDSLKKEAYEVEVHRLLSEAEVLDHSKNPCEDSFLPDTE GHTYVAFIRMEKDDDFTTWTQLAKCLHIWDLDVRGNHRGLWRLFRKKNHFLVVGVPASPY SVKKPPSVTPIFLEPPPKEEGAPGAPEQTLELEVLFQG
>5GGI_2 mannosyl-peptide (chains F, G) XAAPTPVAAPX
| ID | Name | Formula | Copies |
|---|---|---|---|
| MAN | alpha-D-mannopyranose | C6 H12 O6 | 2 |
| PO4 | Phosphate ion | O4 P | 1 |
| MN | Manganese (II) ion | Mn | 2 |
| UDP | Uridine-5'-diphosphate | C9 H14 N2 O12 P2 | 2 |
Carbohydrate-binding domain of the POMGnT1 stem region modulates O-mannosylation sites of alpha-dystroglycan. Kuwabara, N., Manya, H., Yamada, T. et al. Proc Natl Acad Sci U S A (2016) 113:9280-9285. DOI 10.1073/pnas.1525545113 · PubMed
Other PDB entries of the same protein (UniProt Q8WZA1 (AlphaFold model), which also has an AlphaFold model), best resolution first:
MolViewer shows 5GGI directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.