5GGF: PDB entry 5GGF

Crystal structure of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase form II. Determined by X-ray diffraction at 2.49 Å resolution. Released 10 Aug 2016.

Method: X-ray diffraction
Resolution: 2.49 Å
Organism: Homo sapiens
Chains: 3
Atoms: 12,790
Mol. weight: 196.65 kDa
Released: 10 Aug 2016

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

Secondary structure: helices and β-sheets

5GGF contains 80 α-helices and 92 β-strands across 3 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: 29 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	98-105	8	1
β-strand	106	1	2
β-strand	110-114	5	1
β-strand	117-122	6	1
β-strand	130-136	7	2
β-strand	143-149	7	2
α-helix	156-165	10
α-helix	168	1
β-strand	172-178	7	2
α-helix	187-195	9
β-strand	209-215	7	2
β-strand	220-226	7	2
α-helix	234-237	4
β-strand	238-245	8	1
α-helix	246-248	3
α-helix	249-252	4
α-helix	261-269	9
α-helix	276-279	4
α-helix	284-286	3
β-strand	304-308	5	3
α-helix	312-323	12
α-helix	330-332	3
β-strand	333-339	7	3
α-helix	342-351	10
β-strand	354-358	5	3
α-helix	364-382	19
β-strand	388-393	6	3
β-strand	396-398	3	4
α-helix	399	1
α-helix	402-415	14
β-strand	419-423	5	3
β-strand	430	1	5
β-strand	440-443	4	3
β-strand	451-454	4	3
α-helix	455-456	2
α-helix	457-462	6
α-helix	463-465	3
α-helix	466-468	3
α-helix	475-480	6
α-helix	482-485	4
β-strand	489-493	5	3
β-strand	496	1	6
β-strand	498-500	3	4
β-strand	520	1	5
β-strand	522	1	6
α-helix	528-530	3
α-helix	533-536	4
α-helix	538-551	14
α-helix	552	1
β-strand	553-554	2	7
α-helix	555-556	2
β-strand	559	1	8
α-helix	564-566	3
β-strand	574-581	8	7
α-helix	588-596	9
β-strand	607-608	2	7
β-strand	611-616	6	7
β-strand	619-627	9	7
α-helix	630-634	5
β-strand	642	1	7

Chain B: 24 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	98-105	8	9
β-strand	106	1	10
β-strand	110-114	5	9
β-strand	117-122	6	9
β-strand	130-136	7	10
β-strand	143-149	7	10
α-helix	156-164	9
α-helix	168	1
β-strand	172-178	7	10
α-helix	187-195	9
β-strand	209-215	7	10
β-strand	220-226	7	10
α-helix	235-237	3
β-strand	238-245	8	9
α-helix	260-269	10
α-helix	276-279	4
α-helix	284-286	3
β-strand	304-308	5	11
α-helix	312-323	12
α-helix	330-332	3
β-strand	333-337	5	11
α-helix	342-350	9
β-strand	354-357	4	11
α-helix	364-382	19
β-strand	388-393	6	11
β-strand	396-398	3	12
α-helix	399	1
α-helix	402-415	14
β-strand	419-423	5	11
β-strand	430	1	13
β-strand	440-443	4	11
β-strand	451-454	4	11
α-helix	455-457	3
α-helix	458-462	5
α-helix	463-465	3
α-helix	466-468	3
α-helix	475-480	6
α-helix	482-485	4
β-strand	489-493	5	11
β-strand	496	1	14
β-strand	498-500	3	12
β-strand	520	1	13
β-strand	522	1	14
α-helix	528-530	3
α-helix	534-536	3
α-helix	538-551	14
β-strand	553	1	15
β-strand	575-581	7	15
α-helix	588-596	9
β-strand	607-608	2	15
β-strand	611-614	4	15
β-strand	621-627	7	15
α-helix	630-634	5
β-strand	642	1	15

Chain C: 27 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	98-105	8	16
β-strand	106	1	17
β-strand	110-114	5	16
β-strand	117-122	6	16
β-strand	130-136	7	17
β-strand	143-149	7	17
α-helix	156-165	10
α-helix	168	1
β-strand	172-178	7	17
α-helix	187-195	9
β-strand	209-215	7	17
β-strand	220-226	7	17
α-helix	235-237	3
β-strand	238-245	8	16
α-helix	249-252	4
α-helix	261-269	9
α-helix	276-279	4
α-helix	284-286	3
β-strand	304-308	5	18
α-helix	312-323	12
α-helix	330-332	3
β-strand	333-337	5	18
α-helix	342-350	9
β-strand	354-357	4	18
α-helix	364-382	19
β-strand	388-393	6	18
β-strand	396-398	3	19
α-helix	399	1
α-helix	402-415	14
β-strand	419-423	5	18
β-strand	430	1	20
β-strand	440-443	4	18
β-strand	451-454	4	18
α-helix	455-456	2
α-helix	457-462	6
α-helix	463-465	3
α-helix	466-468	3
α-helix	475-479	5
α-helix	482-485	4
β-strand	489-493	5	18
β-strand	496	1	21
β-strand	498-500	3	19
β-strand	520	1	20
β-strand	522	1	21
β-strand	528	1	8
α-helix	529-530	2
α-helix	533-536	4
α-helix	538-551	14
β-strand	553-554	2	22
α-helix	555-556	2
α-helix	564-566	3
β-strand	574-581	8	22
α-helix	588-596	9
β-strand	607-608	2	22
β-strand	611-616	6	22
β-strand	619-627	9	22
α-helix	632-634	3
β-strand	642	1	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1	A, B, C	protein	578	Homo sapiens	Q8WZA1 (AlphaFold model)

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

>5GGF_1 Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1 (chains A, B, C)
GSGPRRVLDVEVYSSRSKVYVAVDGTTVLEDEAREQGRGIHVIVLNQATGHVMAKRVFDT
YSPHEDEAMVLFLNMVAPGRVLICTVKDEGSFHLKDTAKALLRSLGSQAGPALGWRDTWA
FVGRKGGPVFGEKHSKSPALSSWGDPVLLKTDVPLSSAEEAECHWADTELNRRRRRFCSK
VEGYGSVCSCKDPTPIEFSPDPLPDNKVLNVPVAVIAGNRPNYLYRMLRSLLSAQGVSPQ
MITVFIDGYYEEPMDVVALFGLRGIQHTPISIKNARVSQHYKASLTATFNLFPEAKFAVV
LEEDLDIAVDFFSFLSQSIHLLEEDDSLYCISAWNDQGYEHTAEDPALLYRVETMPGLGW
VLRRSLYKEELEPKWPTPEKLWDWDMWMRMPEQRRGRECIIPDVSRSYHFGIVGLNMNGY
FHEAYFKKHKFNTVPGVQLRNVDSLKKEAYEVEVHRLLSEAEVLDHSKNPCEDSFLPDTE
GHTYVAFIRMEKDDDFTTWTQLAKCLHIWDLDVRGNHRGLWRLFRKKNHFLVVGVPASPY
SVKKPPSVTPIFLEPPPKEEGAPGAPEQTLELEVLFQG

Primary citation

Carbohydrate-binding domain of the POMGnT1 stem region modulates O-mannosylation sites of alpha-dystroglycan. Kuwabara, N., Manya, H., Yamada, T. et al. Proc Natl Acad Sci U S A (2016) 113:9280-9285. DOI 10.1073/pnas.1525545113 · PubMed

Other PDB entries of the same protein (UniProt Q8WZA1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5GGN 1.21 Å, Crystal structure of N-terminal domain of human protein O-mannose…
5GGL 1.27 Å, Crystal structure of N-terminal domain of human protein O-mannose…
5GGK 1.3 Å, Crystal structure of N-terminal domain of human protein O-mannose…
5XFC 1.4 Å, Serial femtosecond X-ray structure of a stem domain of human O-mannose…
5GGJ 1.42 Å, Crystal structure of N-terminal domain of human protein O-mannose…
5GGO 1.5 Å, Crystal structure of N-terminal domain of human protein O-mannose…
5GGP 1.6 Å, Crystal structure of N-terminal domain of human protein O-mannose…
5GGI 2.6 Å, Crystal structure of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase in…
5GGG 3.0 Å, Crystal structure of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase…

Browse structure collections

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