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1A49
Biol. Unit 2
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
)
[
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Hetero Components
(2, 7)
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
3
Ligand/Ion
ADENOSINE-5'-TRIPHOSPHATE
2
K
-1
Ligand/Ion
POTASSIUM ION
3
MG
-1
Ligand/Ion
MAGNESIUM ION
4
OXL
4
Ligand/Ion
OXALATE ION
[
close Hetero Component info
]
Sites
(18, 18)
Info
All Sites
01: BC7 (SOFTWARE)
02: BC8 (SOFTWARE)
03: BC9 (SOFTWARE)
04: CC1 (SOFTWARE)
05: CC2 (SOFTWARE)
06: CC3 (SOFTWARE)
07: CC4 (SOFTWARE)
08: CC5 (SOFTWARE)
09: CC6 (SOFTWARE)
10: CC7 (SOFTWARE)
11: CC8 (SOFTWARE)
12: CC9 (SOFTWARE)
13: DC1 (SOFTWARE)
14: DC2 (SOFTWARE)
15: DC3 (SOFTWARE)
16: DC7 (SOFTWARE)
17: DC8 (SOFTWARE)
18: DC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
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
02
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
03
BC9
SOFTWARE
GLU E:3271 , ASP E:3295 , OXL E:3533 , ATP E:3535 , HOH E:6988
BINDING SITE FOR RESIDUE MG E 3534
04
CC1
SOFTWARE
ATP E:3535 , HOH E:6162 , HOH E:6348 , HOH E:7443
BINDING SITE FOR RESIDUE MG E 3536
05
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
06
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
07
CC4
SOFTWARE
GLU F:3871 , ASP F:3895 , OXL F:4133 , ATP F:4135 , HOH F:6460
BINDING SITE FOR RESIDUE MG F 4134
08
CC5
SOFTWARE
ATP F:4135 , HOH F:6300 , HOH F:7054 , HOH F:7055
BINDING SITE FOR RESIDUE MG F 4136
09
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
10
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
11
CC8
SOFTWARE
GLU G:4471 , ASP G:4495 , OXL G:4733 , ATP G:4735 , HOH G:6671
BINDING SITE FOR RESIDUE MG G 4734
12
CC9
SOFTWARE
ATP G:4735 , HOH G:6177 , HOH G:6256 , HOH G:6349
BINDING SITE FOR RESIDUE MG G 4736
13
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
14
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
15
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
16
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
17
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
18
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 only available for the asymmetric unit)
All SNPs/Variants
View:
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Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: PYRUVATE_KINASE (E:3264-3276,F:3864-3876,G:4464-447...)
;
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
4
-
-
-
-
E:3264-3276
F:3864-3876
G:4464-4476
H:5064-5076
[
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]
Exons
(0, 0)
Info
All Exons
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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.
(no "Exon" information available for biological units yet)
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)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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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)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
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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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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select residue range 5 to 10 in chain 'A'
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Asym.Unit (701 KB)
Header - Asym.Unit
Biol.Unit 1 (350 KB)
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