6BW5

Human GPT (DPAGT1) in complex with tunicamycin

Summary for 6BW5

DescriptorUDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase, Tunicamycin, (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate (3 entities in total)
Functional Keywordsn-linked glycosylation, endoplasmic reticulum, tunicamycin, natural product, transferase, transferase-antibiotic complex, transferase/antibiotic
Biological sourceHomo sapiens (Human)
Cellular locationEndoplasmic reticulum membrane; Multi-pass membrane protein Q9H3H5
Total number of polymer chains4
Total molecular weight194907.04
Authors
Yoo, J.,Kuk, A.C.Y.,Mashalidis, E.H.,Lee, S.-Y. (deposition date: 2017-12-14, release date: 2018-02-21, Last modification date: 2018-03-21)
Primary citation
Yoo, J.,Mashalidis, E.H.,Kuk, A.C.Y.,Yamamoto, K.,Kaeser, B.,Ichikawa, S.,Lee, S.Y.
GlcNAc-1-P-transferase-tunicamycin complex structure reveals basis for inhibition of N-glycosylation.
Nat. Struct. Mol. Biol., 25:217-224, 2018
PubMed: 29459785 (PDB entries with the same primary citation)
DOI: 10.1038/s41594-018-0031-y
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (3.1 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.2885008.9%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 6bw5
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Molmil generated image of 6bw5
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Molmil generated image of 6bw5
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More Biological unit images

Molmil generated image of 6bw5
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Molmil generated image of 6bw5
rotated about x axis by 90°
Molmil generated image of 6bw5
rotated about y axis by 90°
(*)In the case of coarse surface representation, the asymmetric unit is shown as red ribbon representation.
Coordinate files for Biological unit (6bw5.pdb2.gz [227.69 KB])
Coordinate files for Biological unit (6bw5.pdb1.gz [227.54 KB])