6IBO: PDB entry 6IBO

Name: PDB 6IBO: Catalytic deficiency of O-GlcNAc transferase leads to X-linked intellectual disability
Published: 2019-07-24
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Catalytic deficiency of O-GlcNAc transferase leads to X-linked intellectual disability. Determined by X-ray diffraction at 2.17 Å resolution. Released 24 Jul 2019.

Method: X-ray diffraction
Resolution: 2.17 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,895
Mol. weight: 82.74 kDa
Ligands: PO4, 12V
Released: 24 Jul 2019

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

Secondary structure: helices and β-sheets

6IBO 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	326-339	14
α-helix	343-356	14
α-helix	361-373	13
α-helix	377-390	14
α-helix	395-407	13
α-helix	411-424	14
α-helix	429-441	13
α-helix	445-458	14
α-helix	463-475	13
α-helix	482-498	17
α-helix	501-503	3
α-helix	507-512	6
α-helix	517-536	20
α-helix	540-545	6
α-helix	550-552	3
β-strand	556-562	7	1
α-helix	569-574	6
α-helix	577-580	4
β-strand	586-592	7	1
α-helix	600-608	9
β-strand	611-614	4	1
α-helix	615-617	3
α-helix	621-631	11
β-strand	635-638	4	1
α-helix	649-652	4
β-strand	658-661	4	1
β-strand	676-679	4	1
α-helix	686-691	6
β-strand	695-698	4	1
α-helix	708-711	4
α-helix	713-715	3
β-strand	719-721	3	2
β-strand	734-737	4	2
α-helix	741-746	6
β-strand	752-755	4	2
β-strand	773-777	5	2
α-helix	781-791	11
β-strand	796-799	4	2
β-strand	802-806	5	2
α-helix	810-813	4
α-helix	815-818	4
β-strand	827-831	5	2
α-helix	832-835	4
β-strand	843-846	4	3
α-helix	850-852	3
α-helix	855-867	13
β-strand	872-877	6	3
α-helix	880-882	3
α-helix	883-893	11
α-helix	897-899	3
β-strand	900-904	5	3
α-helix	908-915	8
β-strand	920-922	3	3
α-helix	931-938	8
β-strand	943-944	2	3
β-strand	945	1	4
α-helix	951-953	3
α-helix	955-963	9
α-helix	966-968	3
β-strand	969	1	4
α-helix	973-985	13
α-helix	987-1003	17
α-helix	1009-1028	20
β-strand	1036	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)
Ala-val-ser-arg-ala	C	protein	9	Homo sapiens

Sequence of entity 1 (A), FASTA

>6IBO_1 UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit (chains A)
GPGSCPTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQ
EALMHYKEAIRISPTFADAYSNMGNTLKEMQDVQGALQCYTRAIQINPAFADAHSNLASI
HKDSGNIPEAIASYRTALKLKPDFPDAYCNLAHCLQIVCDWTDYDERMKKLVSIVADQLE
KNRLPSVHPHHSMLYPLSHGFRKAIAERHGNLCLDKINVLHKPPYEHPKDLKLSDGRLRV
GYVSSDFGKHPTSHLMQSIPGMHNPDKFEVFCYALSPDDGTNFRVKVMAEANHFIDLSQI
PCNGKAADRIHQDGIHILVNMNGYTKGARNELFALRPAPIQAMWLGYPGTSGALFMDYII
TDQETSPAEVAEQYSEKLAYMPHTFFIGDHANMFPHLKKKAVIDFKSNGHIYDNRIVLNG
IDLKAFLDSLPDVKIVKMKCPDGGDNADSSNTALNMPVIPMNTIAEAVIEMINRGQIQIT
INGFSISNGLATTQINNKAATGEEVPRTIIVTTRSQYGLPEDAIVYCNFNQLYKIDPSTL
QMWANILKRVPNSVLWLLRFPAVGEPNIQQYAQNMGLPQNRIIFSPVAPKEEHVRRGQLA
DVCLDTPLCNGHTTGMDVLWAGTPMVTMPGETLASRVAASQLTCLGCLELIAKNRQEYED
IAVKLGTDLEYLKKVRGKVWKQRISSPLFNTKQYTMELERLYLQMWEHYAAGNKPDHMIK
PVE

Sequence of entity 2 (C), FASTA

>6IBO_2 ALA-VAL-SER-ARG-ALA (chains C)
KKVAVSRAA

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	2
12V	(2S,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-t…	C17 H27 N3 O16 P2 S	1

Primary citation

Catalytic deficiency of O-GlcNAc transferase leads to X-linked intellectual disability. Pravata, V.M., Muha, V., Gundogdu, M. et al. Proc Natl Acad Sci U S A (2019) 116:14961-14970. DOI 10.1073/pnas.1900065116 · 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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