5LRD: Glycogen Phosphorylase b

Crystal structure of Glycogen Phosphorylase b in complex with KS242. Determined by X-ray diffraction at 1.8 Å resolution. Released 14 Jun 2017.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Oryctolagus cuniculus
Chains: 1
Atoms: 6,945
Mol. weight: 98.15 kDa
Ligands: PLP, KS2
Released: 14 Jun 2017

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

Secondary structure: helices and β-sheets

5LRD contains 55 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: 55 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	270-273	4
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	576-592	17
β-strand	601-606	6	8
α-helix	608-610	3
α-helix	614-630	17
β-strand	640-645	6	8
α-helix	650-659	10
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	794-806	13
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	843	Oryctolagus cuniculus	P00489 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5LRD_1 Glycogen phosphorylase, muscle form (chains A)
MSRPLSDQEKRKQISVRGLAGVENVTELKKNFNRHLHFTLVKDRNVATPRDYYFALAHTV
RDHLVGRWIRTQQHYYEKDPKRIYYLSLEFYMGRTLQNTMVNLALENACDEATYQLGLDM
EELEEIEEDAGLGNGGLGRLAACFLDSMATLGLAAYGYGIRYEFGIFNQKICGGWQMEEA
DDWLRYGNPWEKARPEFTLPVHFYGRVEHTSQGAKWVDTQVVLAMPYDTPVPGYRNNVVN
TMRLWSAKAPNDFNLKDFNVGGYIQAVLDRNLAENISRVLYPNDNFFEGKELRLKQEYFV
VAATLQDIIRRFKSSKFGCRDPVRTNFDAFPDKVAIQLNDTHPSLAIPELMRVLVDLERL
DWDKAWEVTVKTCAYTNHTVLPEALERWPVHLLETLLPRHLQIIYEINQRFLNRVAAAFP
GDVDRLRRMSLVEEGAVKRINMAHLCIAGSHAVNGVARIHSEILKKTIFKDFYELEPHKF
QNKTNGITPRRWLVLCNPGLAEIIAERIGEEYISDLDQLRKLLSYVDDEAFIRDVAKVKQ
ENKLKFAAYLEREYKVHINPNSLFDVQVKRIHEYKRQLLNCLHVITLYNRIKKEPNKFVV
PRTVMIGGKAAPGYHMAKMIIKLITAIGDVVNHDPVVGDRLRVIFLENYRVSLAEKVIPA
ADLSEQISTAGTEASGTGNMKFMLNGALTIGTMDGANVEMAEEAGEENFFIFGMRVEDVD
RLDQRGYNAQEYYDRIPELRQIIEQLSSGFFSPKQPDLFKDIVNMLMHHDRFKVFADYEE
YVKCQERVSALYKNPREWTRMVIRNIATSGKFSSDRTIAQYAREIWGVEPSRQRLPAPDE
KIP

Ligands and cofactors

ID	Name	Formula	Copies
PLP	Pyridoxal-5'-phosphate	C8 H10 N O6 P	1
KS2	(2~{R},3~{S},4~{R},5~{R},6~{S})-2-(hydroxymethyl)-6-[5-(4-methylphenyl)-4~{H}-1…	C15 H19 N3 O5	1

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

Primary citation

van der Waals interactions govern C-beta-d-glucopyranosyl triazoles' nM inhibitory potency in human liver glycogen phosphorylase. Kantsadi, A.L., Stravodimos, G.A., Kyriakis, E. et al. J Struct Biol (2017) 199:57-67. DOI 10.1016/j.jsb.2017.05.001 · PubMed

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
7ONF 1.6 Å, The binding of p-coumaroyl glucose to glycogen phosphorylase reveals the relationship…
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…

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