9V16: Glycogen phosphorylase

Crystal structure of E. coli glycogen phosphorylase N185A/R267E mutant in complex with AMP. Determined by X-ray diffraction at 3.45 Å resolution. Released 18 Feb 2026.

Method: X-ray diffraction
Resolution: 3.45 Å
Organism: Escherichia coli K-12
Chains: 4
Atoms: 25,769
Mol. weight: 375.9 kDa
Ligands: AMP
Released: 18 Feb 2026

Explore 9V16 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9V16 contains 193 α-helices and 100 β-strands across 4 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: 49 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	12-23	12
α-helix	24-28	5
α-helix	33-35	3
α-helix	38-67	30
β-strand	71-75	5	1
α-helix	85-92	8
α-helix	95-105	11
α-helix	109-114	6
α-helix	117-119	3
α-helix	125-139	15
β-strand	144-149	6	1
β-strand	157-161	5	2
β-strand	164-168	5	2
β-strand	180-192	13	1
β-strand	195-199	5	3
β-strand	202-206	5	3
β-strand	209-221	13	1
β-strand	228-237	10	1
α-helix	263-266	4
α-helix	276-305	30
α-helix	311-314	4
β-strand	315-319	5	1
α-helix	323-326	4
α-helix	327-333	7
α-helix	334-338	5
α-helix	343-353	11
β-strand	354-357	4	1
α-helix	363-365	3
β-strand	368-370	3	4
α-helix	371-377	7
α-helix	379-399	21
α-helix	406-410	5
β-strand	413-414	2	4
β-strand	420-422	3	4
α-helix	423-430	8
β-strand	434-435	2	1
α-helix	439-444	6
α-helix	445-449	5
α-helix	451-456	6
β-strand	461	1	1
β-strand	468	1	5
α-helix	470	1
α-helix	471-476	6
α-helix	480-489	10
α-helix	492-494	3
α-helix	497-506	10
α-helix	512-534	23
β-strand	544-549	6	6
α-helix	558-574	17
α-helix	580-582	3
β-strand	583-588	6	6
α-helix	596-612	17
β-strand	622-627	6	6
α-helix	632-638	7
α-helix	639-641	3
β-strand	644-647	4	6
α-helix	649-650	2
α-helix	659-665	7
β-strand	669-673	5	6
α-helix	677-685	9
α-helix	687-689	3
β-strand	691-693	3	6
α-helix	697-705	9
α-helix	710-716	7
α-helix	718-728	11
α-helix	737-739	3
α-helix	741-748	8
α-helix	756-775	20
α-helix	777-789	13
α-helix	792-794	3
β-strand	795	1	5
α-helix	796-803	8
α-helix	804-808	5

Chain B: 49 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	15-23	9
α-helix	24-29	6
α-helix	33-35	3
α-helix	38-67	30
α-helix	69-70	2
β-strand	71-75	5	7
α-helix	85-92	8
α-helix	95-104	10
α-helix	109-114	6
α-helix	117-119	3
α-helix	127-139	13
β-strand	144-149	6	7
β-strand	157-161	5	8
β-strand	164-168	5	8
α-helix	172-175	4
β-strand	180-192	13	7
β-strand	195-196	2	9
β-strand	199	1	10
β-strand	202	1	10
β-strand	205-206	2	9
β-strand	209-221	13	7
β-strand	228-238	11	7
α-helix	263-266	4
α-helix	276-305	30
α-helix	308-310	3
α-helix	311-314	4
β-strand	315-319	5	7
α-helix	323-326	4
α-helix	327-333	7
α-helix	334-338	5
α-helix	343-353	11
β-strand	354-357	4	7
α-helix	363-365	3
β-strand	368-370	3	11
α-helix	371-377	7
α-helix	379-399	21
α-helix	404-410	7
β-strand	413-414	2	11
β-strand	420-422	3	11
α-helix	423-430	8
β-strand	433-436	4	7
α-helix	439-444	6
α-helix	445-449	5
α-helix	451-456	6
β-strand	461-463	3	7
β-strand	468	1	12
α-helix	470	1
α-helix	471-476	6
α-helix	479-489	11
α-helix	492-494	3
α-helix	497-506	10
α-helix	512-535	24
β-strand	544-549	6	13
α-helix	558-574	17
β-strand	583-588	6	13
α-helix	596-612	17
β-strand	622-627	6	13
α-helix	632-638	7
β-strand	644-647	4	13
α-helix	658-665	8
β-strand	669-673	5	13
α-helix	677-685	9
α-helix	687-689	3
β-strand	691-693	3	13
α-helix	697-705	9
α-helix	710-716	7
α-helix	718-729	12
α-helix	737-740	4
α-helix	741-748	8
α-helix	760-773	14
α-helix	778-790	13
α-helix	791-794	4
β-strand	795	1	12
α-helix	796-802	7
α-helix	803-808	6

Chain C: 46 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	12-23	12
α-helix	24-28	5
α-helix	33-35	3
α-helix	38-67	30
β-strand	71-75	5	14
α-helix	84-92	9
α-helix	95-105	11
α-helix	109-114	6
α-helix	117-119	3
α-helix	125-139	15
β-strand	144-149	6	14
β-strand	157-161	5	15
β-strand	164-168	5	15
α-helix	172-175	4
β-strand	181-192	12	14
β-strand	195-199	5	16
β-strand	202-206	5	16
β-strand	209-221	13	14
α-helix	222	1
β-strand	228-238	11	14
α-helix	276-305	30
α-helix	311-314	4
β-strand	315-319	5	14
α-helix	323-326	4
α-helix	327-337	11
α-helix	343-353	11
β-strand	354-357	4	14
α-helix	363-365	3
β-strand	368-370	3	17
α-helix	371-377	7
α-helix	379-399	21
α-helix	406-410	5
β-strand	413-414	2	17
β-strand	420-422	3	17
α-helix	423-430	8
β-strand	434-435	2	14
α-helix	439-444	6
α-helix	445-449	5
α-helix	451-456	6
β-strand	461	1	14
β-strand	468	1	18
α-helix	470	1
α-helix	471-476	6
α-helix	479-489	11
α-helix	492-494	3
α-helix	497-506	10
α-helix	510-533	24
β-strand	544-549	6	19
α-helix	558-574	17
β-strand	583-588	6	19
α-helix	596-612	17
β-strand	622-627	6	19
α-helix	632-638	7
α-helix	639-641	3
β-strand	644-647	4	19
α-helix	659-665	7
β-strand	669-673	5	19
α-helix	677-685	9
β-strand	691-693	3	19
α-helix	697-705	9
α-helix	711-716	6
α-helix	718-728	11
α-helix	737-740	4
α-helix	741-748	8
α-helix	756-775	20
α-helix	777-789	13
α-helix	792-794	3
β-strand	795	1	18
α-helix	796-803	8
α-helix	804-808	5

Chain D: 49 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	13-27	15
α-helix	38-67	30
α-helix	69-70	2
β-strand	71-75	5	20
α-helix	84-91	8
α-helix	95-104	10
α-helix	109-113	5
α-helix	117-119	3
α-helix	125-139	15
β-strand	144-149	6	20
β-strand	157-161	5	21
β-strand	164-168	5	21
β-strand	180-192	13	20
β-strand	195-196	2	22
β-strand	199	1	23
β-strand	202	1	23
β-strand	205-206	2	22
β-strand	209-221	13	20
β-strand	228-237	10	20
α-helix	263-266	4
α-helix	276-305	30
α-helix	311-314	4
β-strand	315-319	5	20
α-helix	324-326	3
α-helix	327-337	11
α-helix	343-353	11
β-strand	354-356	3	20
α-helix	363-365	3
β-strand	368-370	3	24
α-helix	371-377	7
α-helix	379-399	21
α-helix	404-410	7
β-strand	413-414	2	24
α-helix	415-417	3
β-strand	420-422	3	24
α-helix	423-430	8
β-strand	434-436	3	25
α-helix	439-444	6
α-helix	445-449	5
α-helix	451-456	6
β-strand	461-463	3	25
β-strand	468	1	26
α-helix	470	1
α-helix	471-476	6
α-helix	479-489	11
α-helix	492-494	3
α-helix	497-506	10
α-helix	515-535	21
β-strand	544-549	6	27
α-helix	558-574	17
β-strand	583-588	6	27
α-helix	596-612	17
α-helix	619-621	3
β-strand	622-627	6	27
α-helix	632-638	7
α-helix	639-641	3
β-strand	644-647	4	27
α-helix	649-650	2
α-helix	658-665	8
β-strand	669-673	5	27
α-helix	677-685	9
α-helix	687-689	3
β-strand	691-693	3	27
α-helix	697-705	9
α-helix	710-716	7
α-helix	718-728	11
α-helix	737-740	4
α-helix	741-748	8
α-helix	760-774	15
α-helix	777-788	12
α-helix	791-794	4
β-strand	795	1	26
α-helix	796-802	7
α-helix	803-807	5
α-helix	811-814	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glycogen phosphorylase	A, B, C, D	protein	817	Escherichia coli K-12	P0AC86 (AlphaFold model)

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

>9V16_1 Glycogen phosphorylase (chains A, B, C, D)
MGMNAPFTYSSPTLSVEALKHSIAYKLMFTIGKDPVVANKHEWLNATLFAVRDRLVERWL
RSNRAQLSQETRQVYYLSMEFLIGRTLSNAMLSLGIYEDVQGALEAMGLNLEELIDEEND
PGLGNGGLGRLAACFLDSLATLGLPGRGYGIRYDYGMFKQNIVNGSQKESPDYWLEYGNP
WEFKRHATRYKVRFGGRIQQEGKKTRWIETEEILGVAYDQIIPGYDTDATNTLRLWSAQA
SSEINLGKFNQGDYFAAVEDKNHSENVSEVLYPDDSTYSGRELRLRQEYFLVSSTIQDIL
SRHYQLHKTYDNLADKIAIHLNDTHPVLSIPEMMRLLIDEHQFSWDDAFEVCCQVFSYTN
HTLMSEALETWPVDMLGKILPRHLQIIFEINDYFLKTLQEQYPNDTDLLGRASIIDESNG
RRVRMAWLAVVVSHKVNGVSELHSNLMVQSLFADFAKIFPGRFTNVTNGVTPRRWLAVAN
PSLSAVLDEHLGRNWRTDLSLLNELQQHCDFPMVNHAVHQAKLENKKRLAEYIAQQLNVV
VNPKALFDVQIKRIHEYKRQLMNVLHVITRYNRIKADPDAKWVPRVNIFGGKAASAYYMA
KHIIHLINDVAKVINNDPQIGDKLKVVFIPNYSVSLAQLIIPAADLSEQISLAGTEASGT
SNMKFALNGALTIGTLDGANVEMLDHVGADNIFIFGNTAEEVEELRRQGYKPREYYEKDE
ELHQVLTQIGSGVFSPEDPGRYRDLVDSLINFGDHYQVLADYRSYVDCQDKVDELYELQE
EWTAKAMLNIANMGYFSSDRTIKEYADHIWHIDPVRL

Ligands and cofactors

ID	Name	Formula	Copies
AMP	Adenosine monophosphate	C10 H14 N5 O7 P	4

Primary citation

Structural and mechanistic diversity of glycogen phosphorylases from gut bacteria. Shobu, K., Takai, M., Tanino, H. et al. Proc Natl Acad Sci U S A (2026) 123:e2518513123-e2518513123. DOI 10.1073/pnas.2518513123 · PubMed

Other PDB entries of the same protein (UniProt P0AC86 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9S8K 2.06 Å, Structure of glycogen phosphorylase - tetrameric form - in complex with HPr from…
9S8B 2.79 Å, Structure of glycogen phosphorylase - dimeric form - in complex with HPr from…
9M9P 2.93 Å, Glycogen phosphorylase dimer from E. coli
9S86 2.97 Å, Structure of glycogen phosphorylase - tetrameric form - from Escherichia coli
9S7V 3.1 Å, Structure of glycogen phosphorylase - dimeric form - from Escherichia coli
9UKQ 3.5 Å, Crystal structure of glycogen phosphorylase from Escherichia coli
9UKR 3.55 Å, Crystal structure of glycogen phosphorylase from E. coli in complex with AMP
9V17 3.7 Å, Crystal structure of E. coli glycogen phosphorylase N185A/R267E mutant

Browse structure collections

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