1A5U: Pyruvate kinase

Pyruvate kinase complex with bis MG-ATP-na-oxalate. Determined by X-ray diffraction at 2.35 Å resolution. Released 2 Mar 1999.

Method: X-ray diffraction
Resolution: 2.35 Å
Organism: Oryctolagus cuniculus
Chains: 8
Atoms: 33,890
Mol. weight: 468.26 kDa
Ligands: ATP, MG, OXL
Released: 2 Mar 1999

Explore 1A5U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1A5U contains 201 α-helices and 218 β-strands across 8 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: 26 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	19-21	3
α-helix	25-30	6
β-strand	45-49	5	1
α-helix	52-54	3
α-helix	57-66	10
β-strand	70-74	5	1
α-helix	80-95	16
β-strand	108-112	5	1
β-strand	118-119	2	2
β-strand	120	1	3
β-strand	123	1	4
β-strand	126	1	4
β-strand	133	1	5
β-strand	138-142	5	2
α-helix	145-147	3
β-strand	151	1	4
β-strand	155-157	3	2
β-strand	158	1	3
β-strand	172-175	4	2
β-strand	180-187	8	2
β-strand	191-196	6	2
β-strand	200	1	5
β-strand	207-209	3	2
α-helix	222-233	12
β-strand	238-241	4	1
α-helix	247-257	11
α-helix	259-261	3
β-strand	265-270	6	1
α-helix	273-277	5
α-helix	279-285	7
β-strand	288-292	5	1
α-helix	293-299	7
α-helix	302-304	3
α-helix	305-319	15
β-strand	323-326	4	1
α-helix	331-334	4
α-helix	341-353	13
β-strand	357-360	4	1
α-helix	362-365	4
α-helix	370-386	17
α-helix	390-400	11
α-helix	401-403	3
α-helix	407-422	16
β-strand	426-430	5	6
α-helix	435-442	8
β-strand	449-453	5	6
α-helix	456-461	6
α-helix	462-464	3
β-strand	468-472	5	6
α-helix	476-478	3
α-helix	481-498	18
β-strand	507-512	6	6
β-strand	523-528	6	6

Chain B: 24 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	617-620	4
α-helix	625-630	6
α-helix	637-639	3
β-strand	645-649	5	7
α-helix	657-666	10
β-strand	670-674	5	7
α-helix	680-695	16
β-strand	708-712	5	7
β-strand	719	1	8
β-strand	720	1	9
β-strand	723	1	10
β-strand	726	1	10
β-strand	731-733	3	11
β-strand	738-742	5	12
α-helix	745-747	3
β-strand	751	1	10
β-strand	755-757	3	12
β-strand	758	1	9
α-helix	763-766	4
β-strand	772-775	4	12
β-strand	780-787	8	12
β-strand	791-798	8	12
β-strand	800-802	3	11
β-strand	807	1	8
β-strand	808-809	2	12
α-helix	822-834	13
β-strand	838-841	4	7
α-helix	847-857	11
α-helix	859-861	3
β-strand	865-870	6	7
α-helix	873-877	5
α-helix	879-885	7
β-strand	888-892	5	7
α-helix	893-899	7
α-helix	905-919	15
β-strand	923-926	4	7
α-helix	931-934	4
α-helix	941-953	13
β-strand	957-960	4	7
α-helix	962-965	4
α-helix	970-986	17
α-helix	990-1001	12
α-helix	1007-1021	15
β-strand	1027-1030	4	6
α-helix	1035-1042	8
β-strand	1049-1053	5	6
α-helix	1056-1062	7
β-strand	1068-1072	5	6
α-helix	1076-1078	3
α-helix	1081-1099	19
β-strand	1107-1112	6	6
β-strand	1123-1128	6	6

Chain C: 27 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	1214	1	13
α-helix	1219-1221	3
α-helix	1225-1229	5
β-strand	1237	1	13
α-helix	1238-1239	2
β-strand	1245-1249	5	14
α-helix	1252-1254	3
α-helix	1257-1266	10
β-strand	1270-1274	5	14
α-helix	1280-1295	16
β-strand	1308-1312	5	14
β-strand	1319	1	15
β-strand	1323	1	16
β-strand	1331-1333	3	17
β-strand	1338-1342	5	18
α-helix	1345-1347	3
β-strand	1351	1	16
β-strand	1355-1357	3	18
α-helix	1363-1366	4
β-strand	1372-1375	4	18
β-strand	1380-1387	8	18
β-strand	1391-1396	6	18
β-strand	1400-1402	3	17
β-strand	1407	1	15
β-strand	1408-1409	2	18
α-helix	1422-1434	13
β-strand	1438-1441	4	14
α-helix	1447-1457	11
α-helix	1459-1461	3
β-strand	1465-1470	6	14
α-helix	1473-1477	5
α-helix	1479-1485	7
β-strand	1488-1492	5	14
α-helix	1493-1499	7
α-helix	1502-1504	3
α-helix	1505-1519	15
β-strand	1523-1526	4	14
α-helix	1532-1534	3
α-helix	1541-1553	13
β-strand	1557-1560	4	14
α-helix	1562-1565	4
α-helix	1570-1587	18
α-helix	1590-1601	12
α-helix	1607-1621	15
β-strand	1626-1630	5	19
α-helix	1635-1641	7
β-strand	1649-1653	5	19
α-helix	1656-1661	6
α-helix	1662-1664	3
β-strand	1668-1672	5	19
α-helix	1676-1678	3
α-helix	1681-1699	19
β-strand	1707-1712	6	19
β-strand	1723-1728	6	19

Chain D: 24 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	1817-1820	4
α-helix	1825-1830	6
β-strand	1845-1849	5	20
α-helix	1857-1866	10
β-strand	1870-1874	5	20
α-helix	1880-1895	16
β-strand	1908-1912	5	20
β-strand	1918-1919	2	21
β-strand	1920	1	22
β-strand	1923	1	23
β-strand	1926	1	23
β-strand	1931-1933	3	24
β-strand	1938-1942	5	21
α-helix	1945-1947	3
β-strand	1951	1	23
β-strand	1955-1957	3	21
β-strand	1958	1	22
β-strand	1972-1975	4	21
β-strand	1980-1987	8	21
β-strand	1991-1996	6	21
β-strand	2000-2002	3	24
β-strand	2007-2009	3	21
α-helix	2022-2033	12
β-strand	2038-2041	4	20
α-helix	2047-2057	11
α-helix	2059-2061	3
β-strand	2065-2070	6	20
α-helix	2073-2077	5
α-helix	2079-2085	7
β-strand	2088-2092	5	20
α-helix	2093-2099	7
α-helix	2102-2104	3
α-helix	2105-2119	15
β-strand	2123-2126	4	20
α-helix	2131-2134	4
α-helix	2141-2153	13
β-strand	2157-2160	4	20
α-helix	2162-2165	4
α-helix	2170-2186	17
α-helix	2190-2200	11
α-helix	2207-2221	15
β-strand	2227-2230	4	19
α-helix	2235-2241	7
α-helix	2248	1
β-strand	2249-2253	5	19
α-helix	2256-2261	6
α-helix	2262-2264	3
β-strand	2268-2272	5	19
α-helix	2281-2298	18
β-strand	2307-2312	6	19
β-strand	2323-2328	6	19

Chain E: 24 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	3017-3020	4
α-helix	3025-3030	6
α-helix	3037-3039	3
β-strand	3045-3049	5	25
α-helix	3057-3066	10
β-strand	3070-3074	5	25
α-helix	3080-3095	16
β-strand	3108-3112	5	25
β-strand	3119	1	26
β-strand	3120	1	27
β-strand	3123	1	28
β-strand	3126	1	28
β-strand	3130-3133	4	29
β-strand	3138-3142	5	30
β-strand	3151	1	28
β-strand	3155-3157	3	30
β-strand	3158	1	27
β-strand	3172-3175	4	30
β-strand	3180-3187	8	30
β-strand	3191-3196	6	30
β-strand	3200-3203	4	29
β-strand	3207	1	26
β-strand	3208-3209	2	30
α-helix	3222-3233	12
β-strand	3238-3241	4	25
α-helix	3247-3257	11
α-helix	3259-3261	3
β-strand	3265-3270	6	25
α-helix	3273-3277	5
α-helix	3279-3285	7
β-strand	3288-3292	5	25
α-helix	3293-3299	7
α-helix	3305-3319	15
β-strand	3323-3326	4	25
α-helix	3331-3334	4
α-helix	3341-3353	13
β-strand	3357-3360	4	25
α-helix	3362-3365	4
α-helix	3370-3386	17
α-helix	3390-3400	11
α-helix	3407-3421	15
β-strand	3426-3430	5	31
α-helix	3435-3441	7
α-helix	3448	1
β-strand	3449-3453	5	31
α-helix	3456-3461	6
α-helix	3462-3464	3
β-strand	3468-3472	5	31
α-helix	3476-3478	3
α-helix	3481-3498	18
β-strand	3507-3512	6	31
β-strand	3523-3528	6	31

Chain F: 26 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	3617-3620	4
α-helix	3625-3630	6
α-helix	3637-3639	3
β-strand	3645-3649	5	32
α-helix	3657-3665	9
β-strand	3670-3674	5	32
α-helix	3680-3696	17
β-strand	3708-3712	5	32
β-strand	3719	1	33
β-strand	3720	1	34
β-strand	3723	1	35
β-strand	3731-3733	3	36
α-helix	3734	1
β-strand	3738-3742	5	37
α-helix	3745-3747	3
β-strand	3751	1	35
β-strand	3755-3757	3	37
β-strand	3758	1	34
α-helix	3763-3766	4
β-strand	3772-3775	4	37
β-strand	3780-3787	8	37
β-strand	3791-3798	8	37
β-strand	3800-3802	3	36
β-strand	3807	1	33
β-strand	3808-3809	2	37
α-helix	3822-3833	12
β-strand	3838-3841	4	32
α-helix	3847-3857	11
β-strand	3865-3869	5	32
α-helix	3873-3877	5
α-helix	3879-3885	7
β-strand	3888-3892	5	32
α-helix	3893-3899	7
α-helix	3902-3904	3
α-helix	3905-3919	15
β-strand	3923-3926	4	32
α-helix	3931-3934	4
α-helix	3941-3953	13
β-strand	3957-3960	4	32
α-helix	3962-3965	4
α-helix	3970-3987	18
α-helix	3990-4001	12
α-helix	4007-4021	15
β-strand	4027-4030	4	31
α-helix	4035-4041	7
β-strand	4049-4053	5	31
α-helix	4056-4061	6
α-helix	4062-4064	3
β-strand	4068-4072	5	31
α-helix	4075-4078	4
α-helix	4081-4099	19
β-strand	4107-4112	6	31
β-strand	4123-4128	6	31

Chain G: 25 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	4219-4221	3
α-helix	4225-4230	6
α-helix	4237-4239	3
β-strand	4245-4249	5	38
α-helix	4257-4266	10
β-strand	4270-4274	5	38
α-helix	4280-4295	16
β-strand	4308-4312	5	38
β-strand	4318-4319	2	39
β-strand	4323	1	40
β-strand	4326	1	40
β-strand	4330-4333	4	41
β-strand	4337-4342	6	39
α-helix	4345-4347	3
β-strand	4351	1	40
β-strand	4355-4357	3	39
α-helix	4363-4366	4
β-strand	4372-4375	4	39
β-strand	4380-4387	8	39
β-strand	4391-4396	6	39
β-strand	4400-4403	4	41
β-strand	4407-4409	3	39
α-helix	4422-4433	12
β-strand	4438-4441	4	38
α-helix	4447-4457	11
α-helix	4459-4461	3
β-strand	4465-4470	6	38
α-helix	4473-4477	5
α-helix	4479-4485	7
β-strand	4488-4492	5	38
α-helix	4493-4499	7
α-helix	4502-4504	3
α-helix	4505-4519	15
β-strand	4523-4526	4	38
α-helix	4531-4534	4
α-helix	4541-4553	13
β-strand	4557-4560	4	38
α-helix	4562-4565	4
α-helix	4570-4586	17
α-helix	4590-4601	12
α-helix	4607-4622	16
β-strand	4626-4630	5	42
α-helix	4635-4642	8
β-strand	4649-4653	5	42
α-helix	4656-4662	7
β-strand	4668-4672	5	42
α-helix	4676-4678	3
α-helix	4681-4698	18
β-strand	4707-4712	6	42
β-strand	4723-4728	6	42

Chain H: 25 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	4814	1	43
α-helix	4819-4821	3
α-helix	4825-4830	6
β-strand	4837	1	43
α-helix	4838	1
β-strand	4845-4849	5	44
α-helix	4857-4866	10
β-strand	4870-4874	5	44
α-helix	4880-4896	17
α-helix	4897-4899	3
β-strand	4908-4912	5	44
β-strand	4919	1	45
β-strand	4920	1	46
β-strand	4923	1	47
β-strand	4931-4933	3	48
β-strand	4938-4942	5	49
α-helix	4945-4947	3
β-strand	4951	1	47
β-strand	4955-4957	3	49
β-strand	4958	1	46
α-helix	4963-4966	4
β-strand	4972-4975	4	49
β-strand	4980-4987	8	49
β-strand	4991-4998	8	49
β-strand	5000-5002	3	48
β-strand	5007	1	45
β-strand	5008-5009	2	49
α-helix	5022-5033	12
β-strand	5038-5041	4	44
α-helix	5047-5057	11
β-strand	5065-5069	5	44
α-helix	5073-5077	5
α-helix	5079-5085	7
β-strand	5088-5092	5	44
α-helix	5093-5099	7
α-helix	5102-5104	3
α-helix	5105-5119	15
β-strand	5123-5126	4	44
α-helix	5131-5134	4
α-helix	5141-5153	13
β-strand	5157-5160	4	44
α-helix	5162-5165	4
α-helix	5170-5187	18
α-helix	5190-5200	11
α-helix	5207-5221	15
β-strand	5226-5230	5	42
α-helix	5235-5242	8
β-strand	5249-5253	5	42
α-helix	5256-5262	7
β-strand	5268-5272	5	42
α-helix	5276-5278	3
α-helix	5281-5299	19
β-strand	5307-5312	6	42
β-strand	5323-5328	6	42

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Pyruvate kinase	A, B, C, D, E, F, G, H	protein	530	Oryctolagus cuniculus	P11974 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H), FASTA

>1A5U_1 PYRUVATE KINASE (chains A, B, C, D, E, F, G, H)
SKSHSEAGSAFIQTQQLHAAMADTFLEHMCRLDIDSAPITARNTGIICTIGPASRSVETL
KEMIKSGMNVARMNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVALDTKGPEIRT
GLIKGSGTAEVELKKGATLKITLDNAYMEKCDENILWLDYKNICKVVDVGSKVYVDDGLI
SLQVKQKGPDFLVTEVENGGFLGSKKGVNLPGAAVDLPAVSEKDIQDLKFGVEQDVDMVF
ASFIRKAADVHEVRKILGEKGKNIKIISKIENHEGVRRFDEILEASDGIMVARGDLGIEI
PAEKVFLAQKMIIGRCNRAGKPVICATQMLESMIKKPRPTRAEGSDVANAVLDGADCIML
SGETAKGDYPLEAVRMQHLIAREAEAAMFHRKLFEELARSSSHSTDLMEAMAMGSVEASY
KCLAAALIVLTESGRSAHQVARYRPRAPIIAVTRNHQTARQAHLYRGIFPVVCKDPVQEA
WAEDVDLRVNLAMNVGKARGFFKKGDVVIVLTGWRPGSGFTNTMRVVPVP

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	6
MG	Magnesium ion	Mg	14
OXL	Oxalate ion	C2 O4	8

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

Primary citation

Structure of the bis(Mg2+)-ATP-oxalate complex of the rabbit muscle pyruvate kinase at 2.1 A resolution: ATP binding over a barrel. Larsen, T.M., Benning, M.M., Rayment, I. et al. Biochemistry (1998) 37:6247-6255. DOI 10.1021/bi980243s · PubMed

Other PDB entries of the same protein (UniProt P11974 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2G50 1.65 Å, The location of the allosteric amino acid binding site of muscle pyruvate kinase.
1A49 2.1 Å, Bis MG-ATP-K-oxalate complex of pyruvate kinase
8F6M 2.15 Å, Complex of Rabbit muscle pyruvate kinase with ADP and the phosphonate analogue of PEP…
7R6Y 2.25 Å, E117K mutant pyruvate kinase from rabbit muscle
8F5U 2.3 Å, Rabbit muscle pyruvate kinase in complex with magnesium, potassium and pyruvate
3N25 2.41 Å, The structure of muscle pyruvate kinase in complex with proline, pyruvate, and Mn2+
8F5T 2.41 Å, Rabbit muscle pyruvate kinase in complex with sodium and magnesium
1AQF 2.7 Å, Pyruvate kinase from rabbit muscle with MG, K, and L-phospholactate
1F3X 2.8 Å, S402P mutant of rabbit muscle pyruvate kinase
1PKN 2.9 Å, Structure of rabbit muscle pyruvate kinase complexed with MN2+, K+, and pyruvate
1F3W 3.0 Å, Recombinant rabbit muscle pyruvate kinase

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