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1A49
Asym. Unit
Info
Asym.Unit (701 KB)
Biol.Unit 1 (350 KB)
Biol.Unit 2 (351 KB)
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(1)
Title
:
BIS MG-ATP-K-OXALATE COMPLEX OF PYRUVATE KINASE
Authors
:
T. M. Larsen, M. M. Benning, I. Rayment, G. H. Reed
Date
:
12 Feb 98 (Deposition) - 20 Apr 99 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Keywords
:
Transferase, Pyruvate Kinase, Rabbit Muscle, Domain Movement, Potassium Binding
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. M. Larsen, M. M. Benning, I. Rayment, G. H. Reed
Structure Of The Bis(Mg2+)-Atp-Oxalate Complex Of The Rabbit Muscle Pyruvate Kinase At 2. 1 A Resolution: Atp Binding Over A Barrel.
Biochemistry V. 37 6247 1998
(for further references see the
PDB file header
)
[
close entry info
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Hetero Components
(4, 36)
Info
All Hetero Components
1a: ADENOSINE-5'-TRIPHOSPHATE (ATPa)
1b: ADENOSINE-5'-TRIPHOSPHATE (ATPb)
1c: ADENOSINE-5'-TRIPHOSPHATE (ATPc)
1d: ADENOSINE-5'-TRIPHOSPHATE (ATPd)
1e: ADENOSINE-5'-TRIPHOSPHATE (ATPe)
1f: ADENOSINE-5'-TRIPHOSPHATE (ATPf)
2a: POTASSIUM ION (Ka)
2b: POTASSIUM ION (Kb)
2c: POTASSIUM ION (Kc)
2d: POTASSIUM ION (Kd)
2e: POTASSIUM ION (Ke)
2f: POTASSIUM ION (Kf)
2g: POTASSIUM ION (Kg)
2h: POTASSIUM ION (Kh)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
3e: MAGNESIUM ION (MGe)
3f: MAGNESIUM ION (MGf)
3g: MAGNESIUM ION (MGg)
3h: MAGNESIUM ION (MGh)
3i: MAGNESIUM ION (MGi)
3j: MAGNESIUM ION (MGj)
3k: MAGNESIUM ION (MGk)
3l: MAGNESIUM ION (MGl)
3m: MAGNESIUM ION (MGm)
3n: MAGNESIUM ION (MGn)
4a: OXALATE ION (OXLa)
4b: OXALATE ION (OXLb)
4c: OXALATE ION (OXLc)
4d: OXALATE ION (OXLd)
4e: OXALATE ION (OXLe)
4f: OXALATE ION (OXLf)
4g: OXALATE ION (OXLg)
4h: OXALATE ION (OXLh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ATP
6
Ligand/Ion
ADENOSINE-5'-TRIPHOSPHATE
2
K
8
Ligand/Ion
POTASSIUM ION
3
MG
14
Ligand/Ion
MAGNESIUM ION
4
OXL
8
Ligand/Ion
OXALATE ION
[
close Hetero Component info
]
Sites
(36, 36)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:74 , SER A:76 , ASP A:112 , THR A:113 , SER A:242 , ATP A:535
BINDING SITE FOR RESIDUE K A 532
02
AC2
SOFTWARE
ARG A:72 , LYS A:269 , GLU A:271 , MET A:290 , ALA A:292 , ARG A:293 , GLY A:294 , ASP A:295 , THR A:327 , MG A:534 , ATP A:535 , HOH A:6763
BINDING SITE FOR RESIDUE OXL A 533
03
AC3
SOFTWARE
GLU A:271 , ASP A:295 , OXL A:533 , ATP A:535 , HOH A:6763
BINDING SITE FOR RESIDUE MG A 534
04
AC4
SOFTWARE
ATP A:535 , HOH A:6079 , HOH A:6469
BINDING SITE FOR RESIDUE MG A 536
05
AC5
SOFTWARE
ASN B:674 , SER B:676 , ASP B:712 , THR B:713 , HOH B:6141
BINDING SITE FOR RESIDUE K B 1132
06
AC6
SOFTWARE
LYS B:869 , GLU B:871 , MET B:890 , ALA B:892 , ARG B:893 , GLY B:894 , ASP B:895 , THR B:927 , MG B:1134 , HOH B:6624 , HOH B:7031
BINDING SITE FOR RESIDUE OXL B 1133
07
AC7
SOFTWARE
GLU B:871 , ASP B:895 , OXL B:1133 , HOH B:7031
BINDING SITE FOR RESIDUE MG B 1134
08
AC8
SOFTWARE
ASN C:1274 , SER C:1276 , ASP C:1312 , THR C:1313 , SER C:1442 , ATP C:1735 , HOH C:7921
BINDING SITE FOR RESIDUE K C 1732
09
AC9
SOFTWARE
ARG C:1272 , LYS C:1469 , GLU C:1471 , ALA C:1492 , ARG C:1493 , GLY C:1494 , ASP C:1495 , THR C:1527 , MG C:1734 , ATP C:1735 , HOH C:6663
BINDING SITE FOR RESIDUE OXL C 1733
10
BC1
SOFTWARE
LYS C:1469 , GLU C:1471 , ASP C:1495 , OXL C:1733 , ATP C:1735
BINDING SITE FOR RESIDUE MG C 1734
11
BC2
SOFTWARE
ATP C:1735 , HOH C:6006 , HOH C:6581 , HOH C:6663
BINDING SITE FOR RESIDUE MG C 1736
12
BC3
SOFTWARE
ASN D:1874 , SER D:1876 , ASP D:1912 , THR D:1913 , SER D:2042 , ATP D:2335 , HOH D:7499
BINDING SITE FOR RESIDUE K D 2332
13
BC4
SOFTWARE
LYS D:2069 , GLU D:2071 , MET D:2090 , ALA D:2092 , ARG D:2093 , GLY D:2094 , ASP D:2095 , THR D:2127 , MET D:2159 , MG D:2334 , ATP D:2335 , HOH D:6045 , HOH D:6387
BINDING SITE FOR RESIDUE OXL D 2333
14
BC5
SOFTWARE
GLU D:2071 , ASP D:2095 , OXL D:2333 , ATP D:2335 , HOH D:6439
BINDING SITE FOR RESIDUE MG D 2334
15
BC6
SOFTWARE
ATP D:2335 , HOH D:6045 , HOH D:6387 , HOH D:7364
BINDING SITE FOR RESIDUE MG D 2336
16
BC7
SOFTWARE
ASN E:3074 , SER E:3076 , ASP E:3112 , THR E:3113 , SER E:3242 , ATP E:3535 , HOH E:7785
BINDING SITE FOR RESIDUE K E 3532
17
BC8
SOFTWARE
LYS E:3269 , GLU E:3271 , ALA E:3292 , ARG E:3293 , GLY E:3294 , ASP E:3295 , THR E:3327 , MG E:3534 , ATP E:3535 , HOH E:6162 , HOH E:6348 , HOH E:6988
BINDING SITE FOR RESIDUE OXL E 3533
18
BC9
SOFTWARE
GLU E:3271 , ASP E:3295 , OXL E:3533 , ATP E:3535 , HOH E:6988
BINDING SITE FOR RESIDUE MG E 3534
19
CC1
SOFTWARE
ATP E:3535 , HOH E:6162 , HOH E:6348 , HOH E:7443
BINDING SITE FOR RESIDUE MG E 3536
20
CC2
SOFTWARE
ASN F:3674 , SER F:3676 , ASP F:3712 , THR F:3713 , SER F:3842 , ATP F:4135 , HOH F:6491
BINDING SITE FOR RESIDUE K F 4132
21
CC3
SOFTWARE
ARG F:3672 , LYS F:3869 , GLU F:3871 , MET F:3890 , ALA F:3892 , ARG F:3893 , GLY F:3894 , ASP F:3895 , THR F:3927 , MG F:4134 , ATP F:4135 , HOH F:6300 , HOH F:6460
BINDING SITE FOR RESIDUE OXL F 4133
22
CC4
SOFTWARE
GLU F:3871 , ASP F:3895 , OXL F:4133 , ATP F:4135 , HOH F:6460
BINDING SITE FOR RESIDUE MG F 4134
23
CC5
SOFTWARE
ATP F:4135 , HOH F:6300 , HOH F:7054 , HOH F:7055
BINDING SITE FOR RESIDUE MG F 4136
24
CC6
SOFTWARE
ASN G:4274 , SER G:4276 , ASP G:4312 , THR G:4313 , SER G:4442 , ATP G:4735 , HOH G:7049
BINDING SITE FOR RESIDUE K G 4732
25
CC7
SOFTWARE
ARG G:4272 , LYS G:4469 , GLU G:4471 , ALA G:4492 , ARG G:4493 , GLY G:4494 , ASP G:4495 , THR G:4527 , MG G:4734 , ATP G:4735 , HOH G:6349 , HOH G:6671
BINDING SITE FOR RESIDUE OXL G 4733
26
CC8
SOFTWARE
GLU G:4471 , ASP G:4495 , OXL G:4733 , ATP G:4735 , HOH G:6671
BINDING SITE FOR RESIDUE MG G 4734
27
CC9
SOFTWARE
ATP G:4735 , HOH G:6177 , HOH G:6256 , HOH G:6349
BINDING SITE FOR RESIDUE MG G 4736
28
DC1
SOFTWARE
ASN H:4874 , SER H:4876 , ASP H:4912 , THR H:4913 , HOH H:6838 , HOH H:6965
BINDING SITE FOR RESIDUE K H 5332
29
DC2
SOFTWARE
LYS H:5069 , GLU H:5071 , MET H:5090 , ALA H:5092 , ARG H:5093 , GLY H:5094 , ASP H:5095 , THR H:5127 , MG H:5334 , HOH H:7293
BINDING SITE FOR RESIDUE OXL H 5333
30
DC3
SOFTWARE
LYS H:5069 , GLU H:5071 , ASP H:5095 , OXL H:5333 , HOH H:7292 , HOH H:7293
BINDING SITE FOR RESIDUE MG H 5334
31
DC4
SOFTWARE
PRO A:52 , ARG A:72 , ASN A:74 , HIS A:77 , TYR A:82 , HIS A:83 , ARG A:119 , LYS A:206 , ASP A:295 , SER A:361 , LYS A:366 , K A:532 , OXL A:533 , MG A:534 , MG A:536 , HOH A:6003 , HOH A:6079 , HOH A:6366 , HOH A:6469 , HOH A:6995 , HOH A:7738 , HOH A:7743
BINDING SITE FOR RESIDUE ATP A 535
32
DC5
SOFTWARE
THR C:1249 , PRO C:1252 , ARG C:1272 , ASN C:1274 , HIS C:1277 , TYR C:1282 , HIS C:1283 , ARG C:1319 , LYS C:1406 , ASP C:1495 , SER C:1561 , LYS C:1566 , K C:1732 , OXL C:1733 , MG C:1734 , MG C:1736 , HOH C:6005 , HOH C:6006 , HOH C:6581 , HOH C:6663 , HOH C:6879 , HOH C:7844
BINDING SITE FOR RESIDUE ATP C 1735
33
DC6
SOFTWARE
THR D:1849 , PRO D:1852 , ARG D:1872 , ASN D:1874 , HIS D:1877 , TYR D:1882 , ARG D:1919 , LYS D:2006 , ASP D:2095 , SER D:2161 , LYS D:2166 , K D:2332 , OXL D:2333 , MG D:2334 , MG D:2336 , HOH D:6004 , HOH D:6045 , HOH D:6082 , HOH D:6140 , HOH D:6387 , HOH D:6463 , HOH D:6745 , HOH D:7364 , HOH D:7874
BINDING SITE FOR RESIDUE ATP D 2335
34
DC7
SOFTWARE
THR E:3049 , PRO E:3052 , ARG E:3072 , ASN E:3074 , HIS E:3077 , TYR E:3082 , HIS E:3083 , ARG E:3119 , LYS E:3206 , ASP E:3295 , SER E:3361 , ALA E:3365 , LYS E:3366 , K E:3532 , OXL E:3533 , MG E:3534 , MG E:3536 , HOH E:6159 , HOH E:6162 , HOH E:6222 , HOH E:6318 , HOH E:6348 , HOH E:6498 , HOH E:7137 , HOH E:7443 , HOH E:7793
BINDING SITE FOR RESIDUE ATP E 3535
35
DC8
SOFTWARE
PRO F:3652 , ARG F:3672 , ASN F:3674 , HIS F:3677 , TYR F:3682 , ARG F:3719 , LYS F:3869 , ASP F:3895 , SER F:3961 , LYS F:3966 , K F:4132 , OXL F:4133 , MG F:4134 , MG F:4136 , HOH F:6178 , HOH F:6300 , HOH F:6460 , HOH F:7054 , HOH F:7055 , HOH F:7453 , HOH F:7923
BINDING SITE FOR RESIDUE ATP F 4135
36
DC9
SOFTWARE
THR G:4249 , PRO G:4252 , ARG G:4272 , ASN G:4274 , HIS G:4277 , TYR G:4282 , HIS G:4283 , ARG G:4319 , LYS G:4406 , ASP G:4495 , SER G:4561 , GLY G:4562 , ALA G:4565 , K G:4732 , OXL G:4733 , MG G:4734 , MG G:4736 , HOH G:6177 , HOH G:6179 , HOH G:6256 , HOH G:6349 , HOH G:6534 , HOH G:6637 , HOH G:6671 , HOH G:7330 , HOH G:7663 , HOH G:7924
BINDING SITE FOR RESIDUE ATP G 4735
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 8)
Info
All PROSITE Patterns/Profiles
1: PYRUVATE_KINASE (A:264-276,B:864-876,C:1464-1476,D:...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PYRUVATE_KINASE
PS00110
Pyruvate kinase active site signature.
KPYM_RABIT
265-277
8
A:264-276
B:864-876
C:1464-1476
D:2064-2076
E:3264-3276
F:3864-3876
G:4464-4476
H:5064-5076
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
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Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(3, 24)
Info
All SCOP Domains
1a: SCOP_d1a49a1 (A:116-217)
1b: SCOP_d1a49c1 (C:1316-1417)
1c: SCOP_d1a49d1 (D:1916-2017)
1d: SCOP_d1a49e1 (E:3116-3217)
1e: SCOP_d1a49f1 (F:3716-3817)
1f: SCOP_d1a49g1 (G:4316-4417)
1g: SCOP_d1a49h1 (H:4916-5017)
1h: SCOP_d1a49b1 (B:716-817)
2a: SCOP_d1a49a3 (A:396-530)
2b: SCOP_d1a49c3 (C:1596-1730)
2c: SCOP_d1a49d3 (D:2196-2330)
2d: SCOP_d1a49e3 (E:3396-3530)
2e: SCOP_d1a49f3 (F:3996-4130)
2f: SCOP_d1a49g3 (G:4596-4730)
2g: SCOP_d1a49h3 (H:5196-5330)
2h: SCOP_d1a49b3 (B:996-1130)
3a: SCOP_d1a49a2 (A:12-115,A:218-395)
3b: SCOP_d1a49c2 (C:1212-1315,C:1418-1595)
3c: SCOP_d1a49d2 (D:1812-1915,D:2018-2195)
3d: SCOP_d1a49e2 (E:3012-3115,E:3218-3395)
3e: SCOP_d1a49f2 (F:3612-3715,F:3818-3995)
3f: SCOP_d1a49g2 (G:4212-4315,G:4418-4595)
3g: SCOP_d1a49h2 (H:4812-4915,H:5018-5195)
3h: SCOP_d1a49b2 (B:612-715,B:818-995)
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Classes
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)
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)
Folds
(
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(
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Superfamilies
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(
)
Families
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
PK beta-barrel domain-like
(31)
Superfamily
:
PK beta-barrel domain-like
(31)
Family
:
Pyruvate kinase beta-barrel domain
(28)
Protein domain
:
Pyruvate kinase (PK)
(28)
Rabbit (Oryctolagus cuniculus) [TaxId: 9986]
(7)
1a
d1a49a1
A:116-217
1b
d1a49c1
C:1316-1417
1c
d1a49d1
D:1916-2017
1d
d1a49e1
E:3116-3217
1e
d1a49f1
F:3716-3817
1f
d1a49g1
G:4316-4417
1g
d1a49h1
H:4916-5017
1h
d1a49b1
B:716-817
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Pyruvate kinase C-terminal domain-like
(59)
Superfamily
:
PK C-terminal domain-like
(30)
Family
:
Pyruvate kinase, C-terminal domain
(28)
Protein domain
:
Pyruvate kinase, C-terminal domain
(28)
Rabbit (Oryctolagus cuniculus) [TaxId: 9986]
(7)
2a
d1a49a3
A:396-530
2b
d1a49c3
C:1596-1730
2c
d1a49d3
D:2196-2330
2d
d1a49e3
E:3396-3530
2e
d1a49f3
F:3996-4130
2f
d1a49g3
G:4596-4730
2g
d1a49h3
H:5196-5330
2h
d1a49b3
B:996-1130
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Phosphoenolpyruvate/pyruvate domain
(92)
Family
:
Pyruvate kinase
(28)
Protein domain
:
Pyruvate kinase, N-terminal domain
(28)
Rabbit (Oryctolagus cuniculus) [TaxId: 9986]
(7)
3a
d1a49a2
A:12-115,A:218-395
3b
d1a49c2
C:1212-1315,C:1418-1595
3c
d1a49d2
D:1812-1915,D:2018-2195
3d
d1a49e2
E:3012-3115,E:3218-3395
3e
d1a49f2
F:3612-3715,F:3818-3995
3f
d1a49g2
G:4212-4315,G:4418-4595
3g
d1a49h2
H:4812-4915,H:5018-5195
3h
d1a49b2
B:612-715,B:818-995
[
close SCOP info
]
CATH Domains
(3, 24)
Info
all CATH domains
1a: CATH_1a49A01 (A:12-41,A:385-530)
1b: CATH_1a49C01 (C:1212-1241,C:1585-1730)
1c: CATH_1a49D01 (D:1812-1841,D:2185-2330)
1d: CATH_1a49E01 (E:3012-3041,E:3385-3530)
1e: CATH_1a49F01 (F:3612-3641,F:3985-4130)
1f: CATH_1a49G01 (G:4212-4241,G:4585-4730)
1g: CATH_1a49H01 (H:4812-4841,H:5185-5330)
1h: CATH_1a49B01 (B:612-641,B:985-1130)
2a: CATH_1a49A02 (A:42-115,A:219-384)
2b: CATH_1a49C02 (C:1242-1315,C:1419-1584)
2c: CATH_1a49D02 (D:1842-1915,D:2019-2184)
2d: CATH_1a49E02 (E:3042-3115,E:3219-3384)
2e: CATH_1a49F02 (F:3642-3715,F:3819-3984)
2f: CATH_1a49G02 (G:4242-4315,G:4419-4584)
2g: CATH_1a49H02 (H:4842-4915,H:5019-5184)
2h: CATH_1a49B02 (B:642-715,B:819-984)
3a: CATH_1a49A03 (A:116-218)
3b: CATH_1a49C03 (C:1316-1418)
3c: CATH_1a49D03 (D:1916-2018)
3d: CATH_1a49E03 (E:3116-3218)
3e: CATH_1a49F03 (F:3716-3818)
3f: CATH_1a49G03 (G:4316-4418)
3g: CATH_1a49H03 (H:4916-5018)
3h: CATH_1a49B03 (B:716-818)
View:
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Classes
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Architectures
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Topologies
(
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Homologous Superfamilies
(
)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Pyruvate Kinase; Chain: A, domain 1
(36)
Homologous Superfamily
:
[code=3.40.1380.20, no name defined]
(20)
Rabbit (Oryctolagus cuniculus)
(7)
1a
1a49A01
A:12-41,A:385-530
1b
1a49C01
C:1212-1241,C:1585-1730
1c
1a49D01
D:1812-1841,D:2185-2330
1d
1a49E01
E:3012-3041,E:3385-3530
1e
1a49F01
F:3612-3641,F:3985-4130
1f
1a49G01
G:4212-4241,G:4585-4730
1g
1a49H01
H:4812-4841,H:5185-5330
1h
1a49B01
B:612-641,B:985-1130
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Phosphoenolpyruvate-binding domains
(67)
Rabbit (Oryctolagus cuniculus)
(7)
2a
1a49A02
A:42-115,A:219-384
2b
1a49C02
C:1242-1315,C:1419-1584
2c
1a49D02
D:1842-1915,D:2019-2184
2d
1a49E02
E:3042-3115,E:3219-3384
2e
1a49F02
F:3642-3715,F:3819-3984
2f
1a49G02
G:4242-4315,G:4419-4584
2g
1a49H02
H:4842-4915,H:5019-5184
2h
1a49B02
B:642-715,B:819-984
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
M1 Pyruvate Kinase; Domain 3
(24)
Homologous Superfamily
:
M1 Pyruvate Kinase; Domain 3
(20)
Rabbit (Oryctolagus cuniculus)
(7)
3a
1a49A03
A:116-218
3b
1a49C03
C:1316-1418
3c
1a49D03
D:1916-2018
3d
1a49E03
E:3116-3218
3e
1a49F03
F:3716-3818
3f
1a49G03
G:4316-4418
3g
1a49H03
H:4916-5018
3h
1a49B03
B:716-818
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Asymmetric Unit 1
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