5XFC: PDB entry 5XFC

Serial femtosecond X-ray structure of a stem domain of human O-mannose beta-1,2-N-acetylglucosaminyltransferase solved by Se-SAD using XFEL (refined against 13,000 patterns). Determined by X-ray diffraction at 1.4 Å resolution. Released 30 Aug 2017.

Method: X-ray diffraction
Resolution: 1.4 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,559
Mol. weight: 36.13 kDa
Ligands: MBE
Released: 30 Aug 2017

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

Secondary structure: helices and β-sheets

5XFC contains 12 α-helices and 20 β-strands across 2 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.

Chains A and B: 6 helices, 10 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	156-166	11
α-helix	168	1
β-strand	172-178	7	2
α-helix	187-195	9
α-helix	201-203	3
β-strand	209-215	7	2
β-strand	220-226	7	2
α-helix	235-237	3
β-strand	238-245	8	1
α-helix	246-247	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1	A, B	protein	164	Homo sapiens	Q8WZA1 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5XFC_1 Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1 (chains A, B)
GPLGSGSGPRRVLDVEVYSSRSKVYVAVDGTTVLEDEAREQGRGIHVIVLNQATGHVMAK
RVFDTYSPHEDEAMVLFLNMVAPGRVLICTVKDEGSFHLKDTAKALLRSLGSQAGPALGW
RDTWAFVGRKGGPVFGEKHSKSPALSSWGDPVLLKTDVPLSSAE

Ligands and cofactors

ID	Name	Formula	Copies
MBE	4-nitrophenyl beta-D-mannopyranoside	C12 H15 N O8	2

Primary citation

Experimental phase determination with selenomethionine or mercury-derivatization in serial femtosecond crystallography. Yamashita, K., Kuwabara, N., Nakane, T. et al. IUCrJ (2017) 4:639-647. DOI 10.1107/S2052252517008557 · 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…
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…
5GGF 2.49 Å, Crystal structure of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase…
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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