4XI9: Human OGT

Name: PDB 4XI9: Human OGT in complex with UDP-5S-GlcNAc and substrate peptide (RBL2)
Published: 2015-08-05
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Human OGT in complex with UDP-5S-GlcNAc and substrate peptide (RBL2). Determined by X-ray diffraction at 3.1 Å resolution. Released 5 Aug 2015.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 8
Atoms: 22,400
Mol. weight: 329.37 kDa
Ligands: 12V
Released: 5 Aug 2015

Explore 4XI9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4XI9 contains 173 α-helices and 88 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: 44 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	314-329	16
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	491-493	3
α-helix	500-502	3
α-helix	507-526	20
α-helix	530-533	4
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	611-621	11
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	731-735	5
β-strand	742-745	4	2
β-strand	763-767	5	2
α-helix	771-781	11
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	833-836	4	3
α-helix	840-842	3
α-helix	845-857	13
β-strand	862-866	5	3
α-helix	872-882	11
α-helix	887-889	3
β-strand	890-893	4	3
α-helix	894-897	4
α-helix	898-903	6
α-helix	904-907	4
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	999-1018	20
α-helix	1021-1023	3
β-strand	1026	1	1

Chain B: 43 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	314-329	16
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	453-466	14
α-helix	472-488	17
α-helix	491-493	3
α-helix	500-502	3
α-helix	507-526	20
α-helix	530-533	4
β-strand	546-552	7	5
α-helix	559-564	6
α-helix	567-570	4
β-strand	576-582	7	5
α-helix	590-598	9
β-strand	601-604	4	5
α-helix	605-607	3
α-helix	611-621	11
β-strand	625-628	4	5
α-helix	639-642	4
β-strand	648-652	5	5
β-strand	666-670	5	5
α-helix	676-681	6
β-strand	685-689	5	5
α-helix	698-701	4
α-helix	703-705	3
β-strand	709-711	3	6
β-strand	724-727	4	6
α-helix	731-736	6
β-strand	742-745	4	6
β-strand	763-767	5	6
α-helix	771-781	11
β-strand	786-789	4	6
β-strand	792-796	5	6
α-helix	797-799	3
α-helix	800-803	4
α-helix	805-809	5
β-strand	817-821	5	6
α-helix	823-825	3
β-strand	833-836	4	7
α-helix	840-842	3
α-helix	845-857	13
β-strand	862-866	5	7
α-helix	872-882	11
α-helix	887-889	3
β-strand	890-893	4	7
α-helix	898-904	7
α-helix	905-907	3
β-strand	910-912	3	7
α-helix	921-928	8
β-strand	933-934	2	7
β-strand	935	1	8
α-helix	941-943	3
α-helix	945-953	9
α-helix	956-958	3
β-strand	959	1	8
α-helix	963-975	13
α-helix	977-993	17
α-helix	999-1018	20
α-helix	1021-1023	3
β-strand	1026	1	5

Chain C: 42 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	314-329	16
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	507-526	20
α-helix	530-533	4
β-strand	546-552	7	9
α-helix	559-564	6
α-helix	567-570	4
β-strand	576-582	7	9
α-helix	590-598	9
β-strand	601-604	4	9
α-helix	605-607	3
α-helix	611-621	11
β-strand	625-628	4	9
α-helix	639-642	4
β-strand	648-652	5	9
β-strand	666-670	5	9
α-helix	676-681	6
β-strand	685-689	5	9
α-helix	698-701	4
α-helix	703-705	3
β-strand	709-711	3	10
β-strand	724-727	4	10
α-helix	731-735	5
β-strand	742-745	4	10
β-strand	763-767	5	10
α-helix	771-782	12
β-strand	786-789	4	10
β-strand	792-796	5	10
α-helix	797-799	3
α-helix	800-803	4
α-helix	805-809	5
β-strand	817-821	5	10
α-helix	823-825	3
β-strand	833-836	4	11
α-helix	840-842	3
α-helix	845-857	13
β-strand	862-866	5	11
α-helix	872-882	11
α-helix	887-889	3
β-strand	890-893	4	11
α-helix	898-904	7
α-helix	905-907	3
β-strand	910-912	3	11
α-helix	921-928	8
β-strand	933-934	2	11
β-strand	935	1	12
α-helix	941-943	3
α-helix	945-953	9
α-helix	956-958	3
β-strand	959	1	12
α-helix	963-975	13
α-helix	977-993	17
α-helix	999-1018	20
α-helix	1021-1023	3
β-strand	1026	1	9

Chain D: 44 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	314-329	16
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	453-466	14
α-helix	472-488	17
α-helix	491-493	3
α-helix	500-502	3
α-helix	507-526	20
α-helix	530-533	4
β-strand	546-552	7	13
α-helix	559-564	6
α-helix	567-570	4
β-strand	576-582	7	13
α-helix	590-598	9
β-strand	601-604	4	13
α-helix	605-607	3
α-helix	611-621	11
β-strand	625-628	4	13
α-helix	639-642	4
β-strand	648-652	5	13
β-strand	666-670	5	13
α-helix	676-681	6
β-strand	685-689	5	13
α-helix	698-701	4
α-helix	703-705	3
β-strand	709-711	3	14
β-strand	724-727	4	14
α-helix	731-735	5
β-strand	742-745	4	14
β-strand	763-767	5	14
α-helix	771-781	11
β-strand	786-789	4	14
β-strand	792-796	5	14
α-helix	797-799	3
α-helix	800-803	4
α-helix	805-809	5
β-strand	817-821	5	14
α-helix	823-825	3
β-strand	833-836	4	15
α-helix	840-842	3
α-helix	845-857	13
β-strand	862-866	5	15
α-helix	872-882	11
α-helix	887-889	3
β-strand	890-893	4	15
α-helix	894-897	4
α-helix	898-904	7
α-helix	905-907	3
β-strand	910-912	3	15
α-helix	921-928	8
β-strand	933-934	2	15
β-strand	935	1	16
α-helix	941-943	3
α-helix	945-953	9
α-helix	956-958	3
β-strand	959	1	16
α-helix	963-975	13
α-helix	977-993	17
α-helix	999-1018	20
α-helix	1021-1023	3
β-strand	1026	1	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit	A, B, C, D	protein	723	Homo sapiens	O15294 (AlphaFold model)
Retinoblastoma-like protein 2	E, F, G, H	protein	8	Homo sapiens	Q08999 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>4XI9_1 UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit (chains A, B, C, D)
GPGSCPTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQ
EALMHYKEAIRISPTFADAYSNMGNTLKEMQDVQGALQCYTRAIQINPAFADAHSNLASI
HKDSGNIPEAIASYRTALKLKPDFPDAYCNLAHCLQIVCDWTDYDERMKKLVSIVADQLE
KNRLPSVHPHHSMLYPLSHGFRKAIAERHGNLCLDKINVLHKPPYEHPKDLKLSDGRLRV
GYVSSDFGNHPTSHLMQSIPGMHNPDKFEVFCYALSPDDGTNFRVKVMAEANHFIDLSQI
PCNGKAADRIHQDGIHILVNMNGYTKGARNELFALRPAPIQAMWLGYPGTSGALFMDYII
TDQETSPAEVAEQYSEKLAYMPHTFFIGDHANMFPHLKKKAVIDFKSNGHIYDNRIVLNG
IDLKAFLDSLPDVKIVKMKCPDGGDNADSSNTALNMPVIPMNTIAEAVIEMINRGQIQIT
INGFSISNGLATTQINNKAATGEEVPRTIIVTTRSQYGLPEDAIVYCNFNQLYKIDPSTL
QMWANILKRVPNSVLWLLRFPAVGEPNIQQYAQNMGLPQNRIIFSPVAPKEEHVRRGQLA
DVCLDTPLCNGHTTGMDVLWAGTPMVTMPGETLASRVAASQLTCLGCLELIAKNRQEYED
IAVKLGTDLEYLKKVRGKVWKQRISSPLFNTKQYTMELERLYLQMWEHYAAGNKPDHMIK
PVE

Sequence of entity 2 (E, F, G, H), FASTA

>4XI9_2 Retinoblastoma-like protein 2 (chains E, F, G, H)
VTPVSTAA

Ligands and cofactors

ID	Name	Formula	Copies
12V	(2S,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-t…	C17 H27 N3 O16 P2 S	4

Primary citation

The active site of O-GlcNAc transferase imposes constraints on substrate sequence. Pathak, S., Alonso, J., Schimpl, M. et al. Nat Struct Mol Biol (2015) 22:744-750. DOI 10.1038/nsmb.3063 · 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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