5NPR: The human O-GlcNAc transferase

Name: PDB 5NPR: The human O-GlcNAc transferase in complex with a thiol-linked bisubstrate inhibitor
Published: 2018-05-16
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

The human O-GlcNAc transferase in complex with a thiol-linked bisubstrate inhibitor. Determined by X-ray diffraction at 1.85 Å resolution. Released 16 May 2018.

Method: X-ray diffraction
Resolution: 1.85 Å
Organisms: Homo sapiens, synthetic construct
Chains: 2
Atoms: 5,939
Mol. weight: 81.68 kDa
Ligands: 94T
Released: 16 May 2018

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

Secondary structure: helices and β-sheets

5NPR contains 42 α-helices and 22 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: 42 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	316-330	15
α-helix	333-346	14
α-helix	351-363	13
α-helix	367-380	14
α-helix	385-397	13
α-helix	401-414	14
α-helix	419-431	13
α-helix	435-448	14
α-helix	453-465	13
α-helix	472-488	17
α-helix	491-493	3
α-helix	500-502	3
α-helix	507-525	19
α-helix	526-528	3
α-helix	532-534	3
β-strand	546-552	7	1
α-helix	559-564	6
α-helix	567-570	4
β-strand	576-582	7	1
α-helix	590-598	9
β-strand	601-604	4	1
α-helix	605-607	3
α-helix	611-620	10
β-strand	625-628	4	1
α-helix	639-642	4
β-strand	648-652	5	1
β-strand	666-669	4	1
α-helix	676-681	6
β-strand	685-688	4	1
α-helix	698-701	4
α-helix	703-705	3
β-strand	709-712	4	2
β-strand	724-727	4	2
α-helix	731-736	6
β-strand	742-745	4	2
β-strand	763-768	6	2
α-helix	771-781	11
β-strand	786-789	4	2
β-strand	792-796	5	2
α-helix	800-803	4
α-helix	805-808	4
β-strand	817-821	5	2
α-helix	823-825	3
β-strand	833-835	3	3
α-helix	840-842	3
α-helix	845-857	13
β-strand	862-867	6	3
α-helix	870-872	3
α-helix	873-882	10
α-helix	887-889	3
β-strand	890-894	5	3
α-helix	898-904	7
α-helix	905-907	3
β-strand	910-912	3	3
α-helix	921-928	8
β-strand	933-934	2	3
β-strand	935	1	4
α-helix	941-953	13
α-helix	956-958	3
β-strand	959	1	4
α-helix	963-975	13
α-helix	977-993	17
α-helix	999-1018	20
β-strand	1026	1	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit	A	protein	717	Homo sapiens	O15294 (AlphaFold model)
bisubstrate inhibitor	E	protein	9	synthetic construct

Sequence of entity 1 (A), FASTA

>5NPR_1 UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit (chains A)
THADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHY
KEAIRISPTFADAYSNMGNTLKEMQDVQGALQCYTRAIQINPAFADAHSNLASIHKDSGN
IPEAIASYRTALKLKPDFPDAYCNLAHCLQIVCDWTDYDERMKKLVSIVADQLEKNRLPS
VHPHHSMLYPLSHGFRKAIAERHGNLCLDKINVLHKPPYEHPKDLKLSDGRLRVGYVSSD
FGNHPTSHLMQSIPGMHNPDKFEVFCYALSPDDGTNFRVKVMAEANHFIDLSQIPCNGKA
ADRIHQDGIHILVNMNGYTKGARNELFALRPAPIQAMWLGYPGTSGALFMDYIITDQETS
PAEVAEQYSEKLAYMPHTFFIGDHANMFPHLKKKAVIDFKSNGHIYDNRIVLNGIDLKAF
LDSLPDVKIVKMKCPDGGDNADSSNTALNMPVIPMNTIAEAVIEMINRGQIQITINGFSI
SNGLATTQINNKAATGEEVPRTIIVTTRSQYGLPEDAIVYCNFNQLYKIDPSTLQMWANI
LKRVPNSVLWLLRFPAVGEPNIQQYAQNMGLPQNRIIFSPVAPKEEHVRRGQLADVCLDT
PLCNGHTTGMDVLWAGTPMVTMPGETLASRVAASQLTCLGCLELIAKNRQEYEDIAVKLG
TDLEYLKKVRGKVWKQRISSPLFNTKQYTMELERLYLQMWEHYAAGNKPDHMIKPVE

Sequence of entity 2 (E), FASTA

>5NPR_2 bisubstrate inhibitor (chains E)
XVTPVCTAX

Ligands and cofactors

ID	Name	Formula	Copies
94T	[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(ox…	C12 H20 N2 O12 P2	1

Water and common crystallization additives (K) are not listed.

Primary citation

Thio-Linked UDP-Peptide Conjugates as O-GlcNAc Transferase Inhibitors. Rafie, K., Gorelik, A., Trapannone, R. et al. Bioconjug Chem (2018) 29:1834-1840. DOI 10.1021/acs.bioconjchem.8b00194 · PubMed

Other PDB entries of the same protein (UniProt O15294 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5NPS 1.68 Å, The human O-GlcNAc transferase in complex with a bisubstrate inhibitor
4GYW 1.7 Å, Crystal structure of human O-GlcNAc Transferase in complex with UDP and a glycopeptide
6EOU 1.75 Å, O-GlcNAc transferase TPR domain with the intellectual disability associated mutation L254F
4N39 1.76 Å, Crystal structure of human O-GlcNAc transferase bound to a peptide from HCF-1 pro-repeat…
4GYY 1.85 Å, Crystal structure of human O-GlcNAc Transferase with UDP-5SGlcNAc and a peptide substrate
3TAX 1.88 Å, A Neutral Diphosphate Mimic Crosslinks the Active Site of Human O-GlcNAc Transferase
4N3A 1.88 Å, Crystal Structure of human O-GlcNAc transferase bound to a peptide from HCF-1 pro-repeat…
4GZ3 1.9 Å, Crystal structure of human O-GlcNAc Transferase with UDP and a thioglycopeptide
5LWV 1.9 Å, Human OGT in complex with UDP and fused substrate peptide (HCF1)
6TKA 1.91 Å, Crystal structure of human O-GlcNAc transferase bound to substrate 7 and a peptide from…
3PE4 1.95 Å, Structure of human O-GlcNAc transferase and its complex with a peptide substrate
6MA3 2.0 Å, Crystal structure of human O-GlcNAc transferase bound to a peptide from HCF-1 pro-repeat…

Browse structure collections

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