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3HQP
Biol. Unit 3
Info
Asym.Unit (1.3 MB)
Biol.Unit 1 (102 KB)
Biol.Unit 10 (110 KB)
Biol.Unit 11 (108 KB)
Biol.Unit 12 (105 KB)
Biol.Unit 13 (101 KB)
Biol.Unit 14 (100 KB)
Biol.Unit 15 (99 KB)
Biol.Unit 16 (99 KB)
Biol.Unit 2 (107 KB)
Biol.Unit 3 (105 KB)
Biol.Unit 4 (107 KB)
Biol.Unit 5 (104 KB)
Biol.Unit 6 (103 KB)
Biol.Unit 7 (101 KB)
Biol.Unit 8 (103 KB)
Biol.Unit 9 (108 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF LEISHMANIA MEXICANA PYRUVATE KINASE (LMPYK) IN COMPLEX WITH ATP, OXALATE AND FRUCTOSE 2,6 BISPHOSPHATE
Authors
:
H. P. Morgan, M. D. Walkinshaw
Date
:
08 Jun 09 (Deposition) - 16 Feb 10 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Biol. Unit 5: E (1x)
Biol. Unit 6: F (1x)
Biol. Unit 7: G (1x)
Biol. Unit 8: H (1x)
Biol. Unit 9: I (1x)
Biol. Unit 10: J (1x)
Biol. Unit 11: K (1x)
Biol. Unit 12: L (1x)
Biol. Unit 13: M (1x)
Biol. Unit 14: N (1x)
Biol. Unit 15: O (1x)
Biol. Unit 16: P (1x)
Keywords
:
Tim Barrel, T-State Enzyme, Allosteric Enzyme, Glycolysis, Kinase, Magnesium, Metal-Binding, Pyruvate, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. P. Morgan, I. W. Mcnae, M. W. Nowicki, V. Hannaert, P. A. M. Michels, L. A. Fothergill-Gilmore, M. D. Walkinshaw
The Allosteric Mechanism Of Pryuvate Kinase From Leishmania Mexicana: A Rock And Lock Model
J. Biol. Chem. V. 285 12892 2010
[
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Hetero Components
(3, 3)
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)
1g: ADENOSINE-5'-TRIPHOSPHATE (ATPg)
1h: ADENOSINE-5'-TRIPHOSPHATE (ATPh)
1i: ADENOSINE-5'-TRIPHOSPHATE (ATPi)
1j: ADENOSINE-5'-TRIPHOSPHATE (ATPj)
1k: ADENOSINE-5'-TRIPHOSPHATE (ATPk)
1l: ADENOSINE-5'-TRIPHOSPHATE (ATPl)
1m: ADENOSINE-5'-TRIPHOSPHATE (ATPm)
1n: ADENOSINE-5'-TRIPHOSPHATE (ATPn)
1o: ADENOSINE-5'-TRIPHOSPHATE (ATPo)
2a: FRUCTOSE-2,6-DIPHOSPHATE (FDPa)
2b: FRUCTOSE-2,6-DIPHOSPHATE (FDPb)
2c: FRUCTOSE-2,6-DIPHOSPHATE (FDPc)
2d: FRUCTOSE-2,6-DIPHOSPHATE (FDPd)
2e: FRUCTOSE-2,6-DIPHOSPHATE (FDPe)
2f: FRUCTOSE-2,6-DIPHOSPHATE (FDPf)
2g: FRUCTOSE-2,6-DIPHOSPHATE (FDPg)
2h: FRUCTOSE-2,6-DIPHOSPHATE (FDPh)
2i: FRUCTOSE-2,6-DIPHOSPHATE (FDPi)
2j: FRUCTOSE-2,6-DIPHOSPHATE (FDPj)
2k: FRUCTOSE-2,6-DIPHOSPHATE (FDPk)
2l: FRUCTOSE-2,6-DIPHOSPHATE (FDPl)
2m: FRUCTOSE-2,6-DIPHOSPHATE (FDPm)
2n: FRUCTOSE-2,6-DIPHOSPHATE (FDPn)
2o: FRUCTOSE-2,6-DIPHOSPHATE (FDPo)
2p: FRUCTOSE-2,6-DIPHOSPHATE (FDPp)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
3f: GLYCEROL (GOLf)
4a: POTASSIUM ION (Ka)
4aa: POTASSIUM ION (Kaa)
4ab: POTASSIUM ION (Kab)
4ac: POTASSIUM ION (Kac)
4ad: POTASSIUM ION (Kad)
4ae: POTASSIUM ION (Kae)
4af: POTASSIUM ION (Kaf)
4b: POTASSIUM ION (Kb)
4c: POTASSIUM ION (Kc)
4d: POTASSIUM ION (Kd)
4e: POTASSIUM ION (Ke)
4f: POTASSIUM ION (Kf)
4g: POTASSIUM ION (Kg)
4h: POTASSIUM ION (Kh)
4i: POTASSIUM ION (Ki)
4j: POTASSIUM ION (Kj)
4k: POTASSIUM ION (Kk)
4l: POTASSIUM ION (Kl)
4m: POTASSIUM ION (Km)
4n: POTASSIUM ION (Kn)
4o: POTASSIUM ION (Ko)
4p: POTASSIUM ION (Kp)
4q: POTASSIUM ION (Kq)
4r: POTASSIUM ION (Kr)
4s: POTASSIUM ION (Ks)
4t: POTASSIUM ION (Kt)
4u: POTASSIUM ION (Ku)
4v: POTASSIUM ION (Kv)
4w: POTASSIUM ION (Kw)
4x: POTASSIUM ION (Kx)
4y: POTASSIUM ION (Ky)
4z: POTASSIUM ION (Kz)
5a: MAGNESIUM ION (MGa)
5aa: MAGNESIUM ION (MGaa)
5ab: MAGNESIUM ION (MGab)
5ac: MAGNESIUM ION (MGac)
5ad: MAGNESIUM ION (MGad)
5b: MAGNESIUM ION (MGb)
5c: MAGNESIUM ION (MGc)
5d: MAGNESIUM ION (MGd)
5e: MAGNESIUM ION (MGe)
5f: MAGNESIUM ION (MGf)
5g: MAGNESIUM ION (MGg)
5h: MAGNESIUM ION (MGh)
5i: MAGNESIUM ION (MGi)
5j: MAGNESIUM ION (MGj)
5k: MAGNESIUM ION (MGk)
5l: MAGNESIUM ION (MGl)
5m: MAGNESIUM ION (MGm)
5n: MAGNESIUM ION (MGn)
5o: MAGNESIUM ION (MGo)
5p: MAGNESIUM ION (MGp)
5q: MAGNESIUM ION (MGq)
5r: MAGNESIUM ION (MGr)
5s: MAGNESIUM ION (MGs)
5t: MAGNESIUM ION (MGt)
5u: MAGNESIUM ION (MGu)
5v: MAGNESIUM ION (MGv)
5w: MAGNESIUM ION (MGw)
5x: MAGNESIUM ION (MGx)
5y: MAGNESIUM ION (MGy)
5z: MAGNESIUM ION (MGz)
6a: OXALATE ION (OXLa)
6b: OXALATE ION (OXLb)
6c: OXALATE ION (OXLc)
6d: OXALATE ION (OXLd)
6e: OXALATE ION (OXLe)
6f: OXALATE ION (OXLf)
6g: OXALATE ION (OXLg)
6h: OXALATE ION (OXLh)
6i: OXALATE ION (OXLi)
6j: OXALATE ION (OXLj)
6k: OXALATE ION (OXLk)
6l: OXALATE ION (OXLl)
6m: OXALATE ION (OXLm)
6n: OXALATE ION (OXLn)
6o: OXALATE ION (OXLo)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ATP
1
Ligand/Ion
ADENOSINE-5'-TRIPHOSPHATE
2
FDP
1
Ligand/Ion
FRUCTOSE-2,6-DIPHOSPHATE
3
GOL
-1
Ligand/Ion
GLYCEROL
4
K
-1
Ligand/Ion
POTASSIUM ION
5
MG
-1
Ligand/Ion
MAGNESIUM ION
6
OXL
1
Ligand/Ion
OXALATE ION
[
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Sites
(7, 7)
Info
All Sites
1: BC6 (SOFTWARE)
2: BC7 (SOFTWARE)
3: BC8 (SOFTWARE)
4: BC9 (SOFTWARE)
5: CC1 (SOFTWARE)
6: CC2 (SOFTWARE)
7: CC3 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
BC6
SOFTWARE
HOH C:580 , ATP C:1001 , HOH C:1651
BINDING SITE FOR RESIDUE MG C 500
2
BC7
SOFTWARE
GLU C:240 , ASP C:264 , OXL C:510 , ATP C:1001 , HOH C:1778
BINDING SITE FOR RESIDUE MG C 502
3
BC8
SOFTWARE
ASN C:51 , SER C:53 , ASP C:83 , THR C:84 , SER C:211 , LYS C:238 , ATP C:1001 , HOH C:1131
BINDING SITE FOR RESIDUE K C 504
4
BC9
SOFTWARE
LYS C:238 , GLU C:240 , ALA C:261 , ARG C:262 , GLY C:263 , ASP C:264 , THR C:296 , MG C:502 , ATP C:1001 , HOH C:1778
BINDING SITE FOR RESIDUE OXL C 510
5
CC1
SOFTWARE
LEU C:399 , SER C:400 , ASN C:401 , THR C:402 , ARG C:404 , SER C:405 , LYS C:453 , ARG C:456 , HIS C:480 , ALA C:481 , VAL C:485 , LYS C:486 , GLY C:487 , TYR C:488 , HOH C:506 , HOH C:569 , HOH C:1068 , HOH C:1334
BINDING SITE FOR RESIDUE FDP C 700
6
CC2
SOFTWARE
ARG C:49 , ASN C:51 , HIS C:54 , TYR C:59 , HIS C:60 , ARG C:90 , ARG C:175 , LYS C:238 , ASP C:264 , SER C:330 , GLY C:331 , ALA C:334 , MG C:500 , MG C:502 , K C:504 , OXL C:510 , HOH C:511 , HOH C:580 , HOH C:1181 , HOH C:1458 , HOH C:1651
BINDING SITE FOR RESIDUE ATP C 1001
7
CC3
SOFTWARE
GLN C:354 , SER C:355 , LEU C:357 , GLU C:359
BINDING SITE FOR RESIDUE K C 499
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: PYRUVATE_KINASE (C:233-245)
;
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.
KPYK_LEIME
234-246
1
-
-
C:233-245
-
-
-
-
-
-
-
-
-
-
-
-
-
[
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]
Exons
(0, 0)
Info
All Exons
View:
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(3, 48)
Info
All SCOP Domains
1a: SCOP_d3hqpa2 (A:88-186)
1b: SCOP_d3hqpe2 (E:88-186)
1c: SCOP_d3hqpf2 (F:88-186)
1d: SCOP_d3hqpg2 (G:88-186)
1e: SCOP_d3hqph2 (H:88-186)
1f: SCOP_d3hqpi2 (I:88-186)
1g: SCOP_d3hqpj2 (J:88-186)
1h: SCOP_d3hqpk2 (K:88-186)
1i: SCOP_d3hqpl2 (L:88-186)
1j: SCOP_d3hqpm2 (M:88-186)
1k: SCOP_d3hqpn2 (N:88-186)
1l: SCOP_d3hqpo2 (O:88-186)
1m: SCOP_d3hqpp2 (P:88-186)
1n: SCOP_d3hqpb2 (B:88-186)
1o: SCOP_d3hqpc2 (C:88-186)
1p: SCOP_d3hqpd2 (D:88-186)
2a: SCOP_d3hqpa3 (A:358-498)
2b: SCOP_d3hqpe3 (E:358-498)
2c: SCOP_d3hqpf3 (F:358-498)
2d: SCOP_d3hqpg3 (G:358-498)
2e: SCOP_d3hqph3 (H:358-498)
2f: SCOP_d3hqpi3 (I:358-498)
2g: SCOP_d3hqpj3 (J:358-498)
2h: SCOP_d3hqpk3 (K:358-498)
2i: SCOP_d3hqpl3 (L:358-498)
2j: SCOP_d3hqpm3 (M:358-498)
2k: SCOP_d3hqpn3 (N:358-498)
2l: SCOP_d3hqpo3 (O:358-498)
2m: SCOP_d3hqpp3 (P:358-498)
2n: SCOP_d3hqpb3 (B:358-498)
2o: SCOP_d3hqpc3 (C:358-498)
2p: SCOP_d3hqpd3 (D:358-498)
3a: SCOP_d3hqpa1 (A:1-87,A:187-357)
3b: SCOP_d3hqpe1 (E:1-87,E:187-357)
3c: SCOP_d3hqpf1 (F:1-87,F:187-357)
3d: SCOP_d3hqpg1 (G:1-87,G:187-357)
3e: SCOP_d3hqph1 (H:1-87,H:187-357)
3f: SCOP_d3hqpi1 (I:1-87,I:187-357)
3g: SCOP_d3hqpj1 (J:1-87,J:187-357)
3h: SCOP_d3hqpk1 (K:1-87,K:187-357)
3i: SCOP_d3hqpl1 (L:1-87,L:187-357)
3j: SCOP_d3hqpm1 (M:1-87,M:187-357)
3k: SCOP_d3hqpn1 (N:1-87,N:187-357)
3l: SCOP_d3hqpo1 (O:1-87,O:187-357)
3m: SCOP_d3hqpp1 (P:1-87,P:187-357)
3n: SCOP_d3hqpb1 (B:1-87,B:187-357)
3o: SCOP_d3hqpc1 (C:1-87,C:187-357)
3p: SCOP_d3hqpd1 (D:1-87,D:187-357)
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)
Trypanosome (Leishmania mexicana) [TaxId: 5665]
(11)
1a
d3hqpa2
A:88-186
1b
d3hqpe2
E:88-186
1c
d3hqpf2
F:88-186
1d
d3hqpg2
G:88-186
1e
d3hqph2
H:88-186
1f
d3hqpi2
I:88-186
1g
d3hqpj2
J:88-186
1h
d3hqpk2
K:88-186
1i
d3hqpl2
L:88-186
1j
d3hqpm2
M:88-186
1k
d3hqpn2
N:88-186
1l
d3hqpo2
O:88-186
1m
d3hqpp2
P:88-186
1n
d3hqpb2
B:88-186
1o
d3hqpc2
C:88-186
1p
d3hqpd2
D:88-186
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)
Trypanosome (Leishmania mexicana) [TaxId: 5665]
(11)
2a
d3hqpa3
A:358-498
2b
d3hqpe3
E:358-498
2c
d3hqpf3
F:358-498
2d
d3hqpg3
G:358-498
2e
d3hqph3
H:358-498
2f
d3hqpi3
I:358-498
2g
d3hqpj3
J:358-498
2h
d3hqpk3
K:358-498
2i
d3hqpl3
L:358-498
2j
d3hqpm3
M:358-498
2k
d3hqpn3
N:358-498
2l
d3hqpo3
O:358-498
2m
d3hqpp3
P:358-498
2n
d3hqpb3
B:358-498
2o
d3hqpc3
C:358-498
2p
d3hqpd3
D:358-498
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Phosphoenolpyruvate/pyruvate domain
(92)
Family
:
Pyruvate kinase
(28)
Protein domain
:
Pyruvate kinase, N-terminal domain
(28)
Trypanosome (Leishmania mexicana) [TaxId: 5665]
(11)
3a
d3hqpa1
A:1-87,A:187-357
3b
d3hqpe1
E:1-87,E:187-357
3c
d3hqpf1
F:1-87,F:187-357
3d
d3hqpg1
G:1-87,G:187-357
3e
d3hqph1
H:1-87,H:187-357
3f
d3hqpi1
I:1-87,I:187-357
3g
d3hqpj1
J:1-87,J:187-357
3h
d3hqpk1
K:1-87,K:187-357
3i
d3hqpl1
L:1-87,L:187-357
3j
d3hqpm1
M:1-87,M:187-357
3k
d3hqpn1
N:1-87,N:187-357
3l
d3hqpo1
O:1-87,O:187-357
3m
d3hqpp1
P:1-87,P:187-357
3n
d3hqpb1
B:1-87,B:187-357
3o
d3hqpc1
C:1-87,C:187-357
3p
d3hqpd1
D:1-87,D:187-357
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
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Pfam Domains
(0, 0)
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all PFAM domains
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Asymmetric Unit 1
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Asym.Unit (1.3 MB)
Header - Asym.Unit
Biol.Unit 1 (102 KB)
Header - Biol.Unit 1
Biol.Unit 10 (110 KB)
Header - Biol.Unit 10
Biol.Unit 11 (108 KB)
Header - Biol.Unit 11
Biol.Unit 12 (105 KB)
Header - Biol.Unit 12
Biol.Unit 13 (101 KB)
Header - Biol.Unit 13
Biol.Unit 14 (100 KB)
Header - Biol.Unit 14
Biol.Unit 15 (99 KB)
Header - Biol.Unit 15
Biol.Unit 16 (99 KB)
Header - Biol.Unit 16
Biol.Unit 2 (107 KB)
Header - Biol.Unit 2
Biol.Unit 3 (105 KB)
Header - Biol.Unit 3
Biol.Unit 4 (107 KB)
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Biol.Unit 5 (104 KB)
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Biol.Unit 6 (103 KB)
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Biol.Unit 7 (101 KB)
Header - Biol.Unit 7
Biol.Unit 8 (103 KB)
Header - Biol.Unit 8
Biol.Unit 9 (108 KB)
Header - Biol.Unit 9
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