3FRO: GlgA glycogen synthase

Name: PDB 3FRO: Crystal structure of Pyrococcus abyssi glycogen synthase with open and closed conformations
Published: 2010-01-12
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Crystal structure of Pyrococcus abyssi glycogen synthase with open and closed conformations. Determined by X-ray diffraction at 2.5 Å resolution. Released 12 Jan 2010.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Pyrococcus abyssi
Chains: 3
Atoms: 10,635
Mol. weight: 148.84 kDa
Ligands: NHF, PO4
Released: 12 Jan 2010

Explore 3FRO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3FRO contains 74 α-helices and 61 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: 25 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	1
α-helix	18-31	14
β-strand	35-41	7	1
β-strand	49-56	8	1
β-strand	59-70	12	1
β-strand	73-79	7	1
α-helix	81-84	4
α-helix	92-114	23
α-helix	119-121	3
β-strand	123-127	5	1
α-helix	129-131	3
α-helix	132-142	11
β-strand	146-150	5	1
β-strand	158-159	2	2
α-helix	160-165	6
α-helix	169-171	3
β-strand	176-177	2	2
α-helix	179-186	8
β-strand	189-192	4	1
α-helix	195-200	6
α-helix	202-205	4
α-helix	206-208	3
β-strand	212-214	3	1
α-helix	226-228	3
α-helix	233-244	12
β-strand	250-255	6	3
β-strand	263	1	4
α-helix	265-276	12
α-helix	279-283	5
β-strand	284-289	6	3
α-helix	294-306	13
β-strand	310-313	4	3
α-helix	316-318	3
α-helix	319-326	8
β-strand	331-334	4	3
β-strand	336	1	4
α-helix	343-350	8
α-helix	353	1
β-strand	354-358	5	3
α-helix	362-366	5
β-strand	373-375	3	3
α-helix	380-393	14
α-helix	399-410	12
α-helix	414-426	13
β-strand	432	1	1
β-strand	436	1	5

Chain B: 25 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	6
α-helix	18-31	14
β-strand	35-41	7	6
β-strand	49-56	8	6
β-strand	59-70	12	6
β-strand	73-79	7	6
α-helix	81-84	4
α-helix	92-114	23
α-helix	119-121	3
β-strand	123-127	5	6
α-helix	129-131	3
α-helix	132-142	11
β-strand	146-150	5	6
β-strand	158-159	2	7
α-helix	160-165	6
α-helix	169-171	3
β-strand	176-177	2	7
α-helix	179-186	8
β-strand	189-192	4	6
α-helix	195-200	6
α-helix	202-205	4
α-helix	206-208	3
β-strand	212-214	3	6
α-helix	226-228	3
α-helix	233-243	11
β-strand	250-255	6	8
β-strand	258	1	9
α-helix	265-276	12
α-helix	279-283	5
β-strand	284-289	6	8
β-strand	292	1	9
α-helix	294-306	13
β-strand	310-313	4	8
α-helix	319-328	10
β-strand	331-334	4	8
α-helix	343-351	9
α-helix	353	1
β-strand	354-358	5	8
α-helix	362-366	5
α-helix	369-371	3
β-strand	373-375	3	8
α-helix	380-393	14
α-helix	399-411	13
α-helix	414-426	13
β-strand	436	1	1

Chain C: 24 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	5
α-helix	18-31	14
β-strand	35-41	7	5
β-strand	49-56	8	5
β-strand	59-70	12	5
β-strand	73-79	7	5
α-helix	81-84	4
α-helix	92-114	23
α-helix	119-121	3
β-strand	123-127	5	5
α-helix	129-131	3
α-helix	132-142	11
β-strand	146-150	5	5
β-strand	158-159	2	10
α-helix	160-165	6
α-helix	169-171	3
β-strand	176-177	2	10
α-helix	179-186	8
β-strand	189-192	4	5
α-helix	195-200	6
α-helix	202-205	4
α-helix	206-208	3
β-strand	212-214	3	5
α-helix	226-228	3
α-helix	233-244	12
β-strand	250-255	6	11
β-strand	258	1	12
α-helix	265-275	11
α-helix	279-283	5
β-strand	284-289	6	11
β-strand	292	1	12
α-helix	294-306	13
β-strand	310-313	4	11
α-helix	319-326	8
β-strand	331-334	4	11
α-helix	343-350	8
α-helix	353	1
β-strand	354-358	5	11
α-helix	362-366	5
β-strand	373-375	3	11
α-helix	380-394	15
α-helix	399-411	13
α-helix	414-426	13
β-strand	436	1	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
GlgA glycogen synthase	A, B, C	protein	439	Pyrococcus abyssi	Q9V2J8 (AlphaFold model)

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

>3FRO_1 GlgA glycogen synthase (chains A, B, C)
RHMKVLLLGFEFLPVKVGGLAEALTAISEALASLGHEVLVFTPSHGRFQGEEIGKIRVFG
EEVQVKVSYEERGNLRIYRIGGGLLDSEDVYGPGWDGLIRKAVTFGRASVLLLNDLLREE
PLPDVVHFHDWHTVFAGALIKKYFKIPAVFTIHRLNKSKLPAFYFHEAGLSELAPYPDID
PEHTGGYIADIVTTVSRGYLIDEWGFFRNFEGKITYVFNGIDCSFWNESYLTGSRDERKK
SLLSKFGMDEGVTFMFIGRFDRGQKGVDVLLKAIEILSSKKEFQEMRFIIIGKGDPELEG
WARSLEEKHGNVKVITEMLSREFVRELYGSVDFVIIPSYFEPFGLVALEAMCLGAIPIAS
AVGGLRDIITNETGILVKAGDPGELANAILKALELSRSDLSKFRENCKKRAMSFSWEKSA
ERYVKAYTGSIDRAFDFIL

Ligands and cofactors

ID	Name	Formula	Copies
NHF	1,5-anhydro-D-fructose	C6 H10 O5	1
PO4	Phosphate ion	O4 P	3

Water and common crystallization additives (TRS) are not listed.

Primary citation

Lyase activity of glycogen synthase: Is an elimination/addition mechanism a possible reaction pathway for retaining glycosyltransferases? Diaz, A., Diaz-Lobo, M., Grados, E. et al. IUBMB Life (2012) 64:649-658. DOI 10.1002/iub.1048 · PubMed

Other PDB entries of the same protein (UniProt Q9V2J8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2BFW 1.8 Å, Structure of the C domain of glycogen synthase from Pyrococcus abyssi
5WQC 1.96 Å, Crystal structure of human orexin 2 receptor bound to the selective antagonist EMPA…
6HLP 2.2 Å, Crystal structure of the Neurokinin 1 receptor in complex with the small molecule…
5WS3 2.3 Å, Crystal structures of human orexin 2 receptor bound to the selective antagonist EMPA…
6HLO 2.4 Å, Crystal structure of the Neurokinin 1 receptor in complex with the small molecule…
4S0V 2.5 Å, Crystal structure of the human OX2 orexin receptor bound to the insomnia drug Suvorexant
6FJ3 2.5 Å, High resolution crystal structure of parathyroid hormone 1 receptor in complex with a…
3L01 2.6 Å, Crystal structure of monomeric glycogen synthase from Pyrococcus abyssi
5U09 2.6 Å, High-resolution crystal structure of the human CB1 cannabinoid receptor
6TPN 2.61 Å, Crystal structure of the Orexin-2 receptor in complex with HTL6641 at 2.61 A resolution
7FEE 2.7 Å, Crystal structure of the allosteric modulator ZCZ011 binding to CP55940-bound…
6TPJ 2.74 Å, Crystal structure of the Orexin-2 receptor in complex with suvorexant at 2.76 A resolution

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