7ONF: Glycogen phosphorylase, muscle form

The binding of p-coumaroyl glucose to glycogen phosphorylase reveals the relationship between structural data and effects on cell metabolome. Determined by X-ray diffraction at 1.6 Å resolution. Released 6 Apr 2022.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Oryctolagus cuniculus
Chains: 1
Atoms: 7,160
Mol. weight: 96.2 kDa
Ligands: PLP, IMP, VKK
Released: 6 Apr 2022

Explore 7ONF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7ONF contains 58 α-helices and 29 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: 58 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	14-16	3
α-helix	21-33	13
α-helix	34-38	5
α-helix	48-77	30
α-helix	79-80	2
β-strand	81-85	5	1
β-strand	89-92	4	2
α-helix	95-102	8
α-helix	105-114	10
α-helix	119-123	5
α-helix	127-128	2
β-strand	129-131	3	2
α-helix	135-149	15
β-strand	154-159	6	1
β-strand	163	1	3
α-helix	166	1
β-strand	167-171	5	4
β-strand	174-178	5	4
β-strand	191-192	2	1
α-helix	194-196	3
β-strand	198-202	5	1
β-strand	205-209	5	5
β-strand	212-216	5	5
β-strand	219-231	13	1
β-strand	238-247	10	1
α-helix	262-267	6
α-helix	269-273	5
α-helix	274-276	3
β-strand	278	1	3
α-helix	290-312	23
α-helix	326-328	3
α-helix	329-332	4
β-strand	333-338	6	1
α-helix	345-351	7
α-helix	352-356	5
α-helix	361-371	11
β-strand	372-375	4	1
α-helix	381-383	3
β-strand	386-388	3	6
α-helix	389-395	7
α-helix	397-417	21
α-helix	422-428	7
β-strand	431-432	2	6
α-helix	433	1
β-strand	438-440	3	6
α-helix	441-447	7
β-strand	451-454	4	1
α-helix	457-465	9
α-helix	469-474	6
α-helix	476-478	3
β-strand	479-481	3	1
β-strand	486	1	7
α-helix	488	1
α-helix	489-494	6
α-helix	497-507	11
α-helix	510-513	4
α-helix	515-524	10
α-helix	528-553	26
β-strand	562-567	6	8
α-helix	572-574	3
α-helix	576-592	17
β-strand	601-606	6	8
α-helix	608-610	3
α-helix	614-630	17
α-helix	637-639	3
β-strand	640-645	6	8
α-helix	650-656	7
α-helix	657-659	3
β-strand	662-665	4	8
α-helix	667-668	2
α-helix	677-683	7
β-strand	687-690	4	8
α-helix	696-703	8
α-helix	705-707	3
β-strand	709-710	2	8
α-helix	715-724	10
α-helix	728-734	7
α-helix	736-747	12
α-helix	759-767	9
α-helix	774-776	3
α-helix	777-791	15
α-helix	794-805	12
α-helix	809-811	3
β-strand	812	1	7
α-helix	813-820	8
α-helix	821-825	5
α-helix	832-835	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glycogen phosphorylase, muscle form	A	protein	825	Oryctolagus cuniculus	P00489 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7ONF_1 Glycogen phosphorylase, muscle form (chains A)
QISVRGLAGVENVTELKKNFNRHLHFTLVKDRNVATPRDYYFALAHTVRDHLVGRWIRTQ
QHYYEKDPKRIYYLSLEFYMGRTLQNTMVNLALENACDEATYQLGLDMEELEEIEEDAGL
GNGGLGRLAACFLDSMATLGLAAYGYGIRYEFGIFNQKICGGWQMEEADDWLRYGNPWEK
ARPEFTLPVHFYGRVEHTSQGAKWVDTQVVLAMPYDTPVPGYRNNVVNTMRLWSAKAPND
FNLKDFNVGGYIQAVLDRNLAENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRF
KSSKFGCRDPVRTNFDAFPDKVAIQLNDTHPSLAIPELMRVLVDLERLDWDKAWEVTVKT
CAYTNHTVLPEALERWPVHLLETLLPRHLQIIYEINQRFLNRVAAAFPGDVDRLRRMSLV
EEGAVKRINMAHLCIAGSHAVNGVARIHSEILKKTIFKDFYELEPHKFQNKTNGITPRRW
LVLCNPGLAEIIAERIGEEYISDLDQLRKLLSYVDDEAFIRDVAKVKQENKLKFAAYLER
EYKVHINPNSLFDVQVKRIHEYKRQLLNCLHVITLYNRIKKEPNKFVVPRTVMIGGKAAP
GYHMAKMIIKLITAIGDVVNHDPVVGDRLRVIFLENYRVSLAEKVIPAADLSEQISTAGT
EASGTGNMKFMLNGALTIGTMDGANVEMAEEAGEENFFIFGMRVEDVDRLDQRGYNAQEY
YDRIPELRQIIEQLSSGFFSPKQPDLFKDIVNMLMHHDRFKVFADYEEYVKCQERVSALY
KNPREWTRMVIRNIATSGKFSSDRTIAQYAREIWGVEPSRQRLPA

Ligands and cofactors

ID	Name	Formula	Copies
PLP	Pyridoxal-5'-phosphate	C8 H10 N O6 P	1
IMP	Inosinic acid	C10 H13 N4 O8 P	1
VKK	p-coumaroyl glucose	C15 H18 O8	1

Primary citation

Structure activity relationship of the binding of p-coumaroyl glucose to glycogen phosphorylase and its effect on hepatic cell metabolic pathways. Tsagkarakou, A.S., Chasapi, S.A., Koulas, S.M. et al. Eur J Med Chem Rep (2021) 3:100011. DOI 10.1016/j.ejmcr.2021.100011

Other PDB entries of the same protein (UniProt P00489 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7P7D 1.45 Å, Rabbit muscle Glycogen Phosphorylase T state
2GJ4 1.6 Å, Structure of rabbit muscle glycogen phosphorylase in complex with ligand
5LRF 1.75 Å, Crystal structure of Glycogen Phosphorylase b in complex with KS389
1C8K 1.76 Å, Flavopiridol inhibits glycogen phosphorylase by binding at the inhibitor site
1H5U 1.76 Å, The 1.76 a resolution crystal structure of glycogen phosphorylase B complexed with…
1A8I 1.78 Å, Spirohydantoin inhibitor of glycogen phosphorylase
5MEM 1.78 Å, A potent fluorescent inhibitor of glycogen phosphorylase as a catalytic site probe.
1K06 1.8 Å, Crystallographic Binding Study of 100 mM N-benzoyl-N'-beta-D-glucopyranosyl urea to…
1WW3 1.8 Å, Crystallographic studies on two bioisosteric analogues,…
2QNB 1.8 Å, Glycogen Phosphorylase b in complex with N-benzoyl-N'-beta-D-glucopyranosyl urea
2QRQ 1.8 Å, Glycogen Phosphorylase b in complex with (1R)-3'-(4-methylphenyl)-spiro[1,5-anhydro-D-glu…
4YI3 1.8 Å, Crystal structure of Gpb in complex with 4a

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