6MA4: Human O-GlcNAc transferase

Crystal structure of human O-GlcNAc transferase bound to a peptide from HCF-1 pro-repeat 2 (11-26) and inhibitor 3a. Determined by X-ray diffraction at 2.0 Å resolution. Released 17 Oct 2018.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 2
Atoms: 6,064
Mol. weight: 83.21 kDa
Ligands: JA7
Released: 17 Oct 2018

Explore 6MA4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6MA4 contains 46 α-helices and 22 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.

Chain A: 44 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	314-330	17
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	419-432	14
α-helix	435-448	14
α-helix	453-465	13
α-helix	472-488	17
α-helix	497-500	4
α-helix	507-526	20
α-helix	530-534	5
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	666-670	5	1
α-helix	676-681	6
β-strand	685-689	5	1
α-helix	698-701	4
α-helix	703-705	3
β-strand	709-711	3	2
β-strand	724-727	4	2
α-helix	731-736	6
β-strand	742-744	3	2
β-strand	764-767	4	2
α-helix	771-782	12
β-strand	786-789	4	2
β-strand	792-796	5	2
α-helix	797-799	3
α-helix	800-803	4
α-helix	805-809	5
β-strand	817-821	5	2
α-helix	822-825	4
β-strand	832-835	4	3
α-helix	840-842	3
α-helix	845-857	13
β-strand	861-866	6	3
α-helix	870-872	3
α-helix	873-882	10
α-helix	887-889	3
β-strand	890-893	4	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	941-943	3
α-helix	945-953	9
α-helix	956-958	3
β-strand	959	1	4
α-helix	963-975	13
α-helix	977-993	17
α-helix	995-997	3
α-helix	999-1018	20
α-helix	1021-1023	3
β-strand	1026	1	1

Chain B: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	12-15	4
α-helix	20-23	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit	A	protein	723	Homo sapiens	O15294 (AlphaFold model)
Host Cell Factor 1 peptide	B	protein	16	Homo sapiens	P51610 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6MA4_1 UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit (chains A)
GPGSCPTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQ
EALMHYKEAIRISPTFADAYSNMGNTLKEMQDVQGALQCYTRAIQINPAFADAHSNLASI
HKDSGNIPEAIASYRTALKLKPDFPDAYCNLAHCLQIVCDWTDYDERMKKLVSIVADQLE
KNRLPSVHPHHSMLYPLSHGFRKAIAERHGNLCLDKINVLHKPPYEHPKDLKLSDGRLRV
GYVSSDFGNHPTSHLMQSIPGMHNPDKFEVFCYALSPDDGTNFRVKVMAEANHFIDLSQI
PCNGKAADRIHQDGIHILVNMNGYTKGARNELFALRPAPIQAMWLGYPGTSGALFMDYII
TDQETSPAEVAEQYSEKLAYMPHTFFIGDHANMFPHLKKKAVIDFKSNGHIYDNRIVLNG
IDLKAFLDSLPDVKIVKMKCPDGGDNADSSNTALNMPVIPMNTIAEAVIEMINRGQIQIT
INGFSISNGLATTQINNKAATGEEVPRTIIVTTRSQYGLPEDAIVYCNFNQLYKIDPSTL
QMWANILKRVPNSVLWLLRFPAVGEPNIQQYAQNMGLPQNRIIFSPVAPKEEHVRRGQLA
DVCLDTPLCNGHTTGMDVLWAGTPMVTMPGETLASRVAASQLTCLGCLELIAKNRQEYED
IAVKLGTDLEYLKKVRGKVWKQRISSPLFNTKQYTMELERLYLQMWEHYAAGNKPDHMIK
PVE

Sequence of entity 2 (B), FASTA

>6MA4_2 Host Cell Factor 1 peptide (chains B)
THETGTTNTATTATSN

Ligands and cofactors

ID	Name	Formula	Copies
JA7	5-{2-[(1R)-2-{(carboxymethyl)[(thiophen-2-yl)methyl]amino}-2-oxo-1-{[(2-oxo-1,2…	C29 H29 N3 O9 S2	1

Primary citation

Structure-Based Evolution of Low Nanomolar O-GlcNAc Transferase Inhibitors. Martin, S.E.S., Tan, Z.W., Itkonen, H.M. et al. J Am Chem Soc (2018) 140:13542-13545. DOI 10.1021/jacs.8b07328 · 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
5NPR 1.85 Å, The human O-GlcNAc transferase in complex with a thiol-linked bisubstrate inhibitor
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

Browse structure collections

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