3PE4: PDB entry 3PE4

Name: PDB 3PE4: Structure of human O-GlcNAc transferase and its complex with a peptide substrate
Published: 2011-01-19
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Structure of human O-GlcNAc transferase and its complex with a peptide substrate. Determined by X-ray diffraction at 1.95 Å resolution. Released 19 Jan 2011.

Method: X-ray diffraction
Resolution: 1.95 Å
Organism: Homo sapiens
Chains: 4
Atoms: 12,036
Mol. weight: 165.84 kDa
Ligands: UDP
Released: 19 Jan 2011

Explore 3PE4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3PE4 contains 87 α-helices and 48 β-strands across 4 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: 43 helices, 23 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	497-502	6
α-helix	507-526	20
α-helix	530-536	7
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
β-strand	633	1	2
α-helix	639-642	4
β-strand	648-651	4	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	3
β-strand	724-727	4	3
α-helix	731-736	6
β-strand	742-745	4	3
β-strand	763-768	6	3
α-helix	771-782	12
β-strand	786-789	4	3
β-strand	792-796	5	3
α-helix	797-799	3
α-helix	800-803	4
α-helix	805-808	4
β-strand	817-821	5	3
α-helix	822-825	4
β-strand	832-835	4	4
α-helix	840-842	3
α-helix	845-857	13
β-strand	861-867	7	4
α-helix	870-872	3
α-helix	873-882	10
α-helix	887-889	3
β-strand	890-894	5	4
α-helix	898-904	7
α-helix	905-907	3
β-strand	910-912	3	4
α-helix	921-928	8
β-strand	933-934	2	4
β-strand	935	1	5
α-helix	941-943	3
α-helix	945-953	9
α-helix	956-958	3
β-strand	959	1	5
α-helix	963-975	13
α-helix	977-993	17
α-helix	999-1018	20
α-helix	1021-1023	3
β-strand	1026	1	1

Chains B and D: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	23	1	2
α-helix	24-25	2

Chain C: 42 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	337-346	10
α-helix	351-364	14
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	497-502	6
α-helix	507-526	20
α-helix	530-536	7
β-strand	546-552	7	6
α-helix	559-564	6
α-helix	567-570	4
β-strand	576-582	7	6
α-helix	590-598	9
β-strand	601-604	4	6
α-helix	605-607	3
α-helix	611-620	10
β-strand	625-628	4	6
β-strand	633	1	7
α-helix	639-642	4
β-strand	648-652	5	6
β-strand	666-669	4	6
α-helix	676-681	6
β-strand	685-688	4	6
α-helix	698-701	4
α-helix	703-705	3
β-strand	709-712	4	8
β-strand	724-727	4	8
α-helix	731-736	6
β-strand	742-745	4	8
β-strand	763-768	6	8
α-helix	771-782	12
β-strand	786-789	4	8
β-strand	792-796	5	8
α-helix	797-799	3
α-helix	800-803	4
α-helix	805-808	4
β-strand	817-821	5	8
α-helix	822-824	3
β-strand	832-835	4	9
α-helix	840-842	3
α-helix	845-857	13
β-strand	861-867	7	9
α-helix	870-872	3
α-helix	873-882	10
α-helix	887-889	3
β-strand	890-894	5	9
α-helix	898-904	7
α-helix	905-907	3
β-strand	910-912	3	9
α-helix	921-928	8
β-strand	933-934	2	9
β-strand	935	1	10
α-helix	941-943	3
α-helix	945-953	9
α-helix	956-958	3
β-strand	959	1	10
α-helix	963-975	13
α-helix	977-993	17
α-helix	999-1018	20
α-helix	1021-1023	3
β-strand	1026	1	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit	A, C	protein	723	Homo sapiens	O15294 (AlphaFold model)
Casein kinase II subunit alpha	B, D	protein	14	Homo sapiens	P68400 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>3PE4_1 UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit (chains A, C)
GPGSCPTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQ
EALMHYKEAIRISPTFADAYSNMGNTLKEMQDVQGALQCYTRAIQINPAFADAHSNLASI
HKDSGNIPEAIASYRTALKLKPDFPDAYCNLAHCLQIVCDWTDYDERMKKLVSIVADQLE
KNRLPSVHPHHSMLYPLSHGFRKAIAERHGNLCLDKINVLHKPPYEHPKDLKLSDGRLRV
GYVSSDFGNHPTSHLMQSIPGMHNPDKFEVFCYALSPDDGTNFRVKVMAEANHFIDLSQI
PCNGKAADRIHQDGIHILVNMNGYTKGARNELFALRPAPIQAMWLGYPGTSGALFMDYII
TDQETSPAEVAEQYSEKLAYMPHTFFIGDHANMFPHLKKKAVIDFKSNGHIYDNRIVLNG
IDLKAFLDSLPDVKIVKMKCPDGGDNADSSNTALNMPVIPMNTIAEAVIEMINRGQIQIT
INGFSISNGLATTQINNKAATGEEVPRTIIVTTRSQYGLPEDAIVYCNFNQLYKIDPSTL
QMWANILKRVPNSVLWLLRFPAVGEPNIQQYAQNMGLPQNRIIFSPVAPKEEHVRRGQLA
DVCLDTPLCNGHTTGMDVLWAGTPMVTMPGETLASRVAASQLTCLGCLELIAKNRQEYED
IAVKLGTDLEYLKKVRGKVWKQRISSPLFNTKQYTMELERLYLQMWEHYAAGNKPDHMIK
PVE

Sequence of entity 2 (B, D), FASTA

>3PE4_2 Casein kinase II subunit alpha (chains B, D)
YPGGSTPVSSANMM

Ligands and cofactors

ID	Name	Formula	Copies
UDP	Uridine-5'-diphosphate	C9 H14 N2 O12 P2	2

Water and common crystallization additives (SO4) are not listed.

Primary citation

Structure of human O-GlcNAc transferase and its complex with a peptide substrate. Lazarus, M.B., Nam, Y., Jiang, J. et al. Nature (2011) 469:564-567. DOI 10.1038/nature09638 · 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…
6MA3 2.0 Å, Crystal structure of human O-GlcNAc transferase bound to a peptide from HCF-1 pro-repeat…

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