5C1D: Human OGT

Name: PDB 5C1D: Human OGT in complex with UDP-5S-GlcNAc and substrate peptide (RB2L)
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 (RB2L). Determined by X-ray diffraction at 2.05 Å resolution. Released 5 Aug 2015.

Method: X-ray diffraction
Resolution: 2.05 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,865
Mol. weight: 82.53 kDa
Ligands: 12V, PO4
Released: 5 Aug 2015

Explore 5C1D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5C1D contains 43 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: 43 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	316-329	14
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	497-502	6
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	611-621	11
β-strand	625-628	4	1
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	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	797-799	3
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	873-881	9
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	941-943	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
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	723	Homo sapiens	O15294 (AlphaFold model)
Retinoblastoma-like protein 2	C	protein	8	Homo sapiens	Q08999 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5C1D_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 (C), FASTA

>5C1D_2 Retinoblastoma-like protein 2 (chains C)
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	1
PO4	Phosphate ion	O4 P	2

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

About this viewer

MolViewer shows 5C1D directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.