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3QV7
Asym. Unit
Info
Asym.Unit (295 KB)
Biol.Unit 1 (288 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF LEISHMANIA MEXICANA PYRUVATE KINASE(LMPYK)IN COMPLEX WITH PONCEAU S AND ACID BLUE 25.
Authors
:
H. P. Morgan, D. S. Auld, I. W. Mcnae, M. W. Nowicki, P. A. M. Michels, L. A. Fothergill-Gilmore, M. D. Walkinshaw
Date
:
25 Feb 11 (Deposition) - 29 Jun 11 (Release) - 21 Sep 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Pyruvate Kinase, Glycolysis, Tim Barrel, Sugar Kinase, Adp/Atp Binding, Cytosol, Transferase-Transferase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. P. Morgan, I. W. Mcnae, M. W. Nowicki, W. Zhong, P. A. Michels, D. S. Auld, L. A. Fothergill-Gilmore, M. D. Walkinshaw
The Trypanocidal Drug Suramin And Other Trypan Blue Mimetic Are Inhibitors Of Pyruvate Kinases And Bind To The Adenosin Site.
J. Biol. Chem. V. 286 31232 2011
[
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Hetero Components
(4, 18)
Info
All Hetero Components
1a: POTASSIUM ION (Ka)
1b: POTASSIUM ION (Kb)
1c: POTASSIUM ION (Kc)
1d: POTASSIUM ION (Kd)
1e: POTASSIUM ION (Ke)
1f: POTASSIUM ION (Kf)
1g: POTASSIUM ION (Kg)
1h: POTASSIUM ION (Kh)
2a: 3-HYDROXY-4-[(E)-{2-SULFO-4-[(E)-(... (QV7a)
2b: 3-HYDROXY-4-[(E)-{2-SULFO-4-[(E)-(... (QV7b)
2c: 3-HYDROXY-4-[(E)-{2-SULFO-4-[(E)-(... (QV7c)
2d: 3-HYDROXY-4-[(E)-{2-SULFO-4-[(E)-(... (QV7d)
2e: 3-HYDROXY-4-[(E)-{2-SULFO-4-[(E)-(... (QV7e)
3a: 9,10-DIOXO-4-(PHENYLAMINO)-9,10-DI... (QV8a)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
K
8
Ligand/Ion
POTASSIUM ION
2
QV7
5
Ligand/Ion
3-HYDROXY-4-[(E)-{2-SULFO-4-[(E)-(4-SULFOPHENYL)DIAZENYL]PHENYL}DIAZENYL]NAPHTHALENE-2,7-DISULFONICACID
3
QV8
1
Ligand/Ion
9,10-DIOXO-4-(PHENYLAMINO)-9,10-DIHYDROANTHRACENE-2-SULFONIC ACID
4
SO4
4
Ligand/Ion
SULFATE ION
[
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Sites
(17, 17)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PRO D:87 , GLU D:88 , ILE D:89 , VAL D:177 , ASN D:178 , PHE D:212
BINDING SITE FOR RESIDUE SO4 D 499
02
AC2
SOFTWARE
SER D:400 , ASN D:401 , THR D:402 , ARG D:404 , SER D:405 , ALA D:481 , ASP D:482
BINDING SITE FOR RESIDUE SO4 D 500
03
AC3
SOFTWARE
ASN D:51 , SER D:53 , THR D:84 , LYS D:238
BINDING SITE FOR RESIDUE K D 501
04
AC4
SOFTWARE
ASP D:264
BINDING SITE FOR RESIDUE K D 502
05
AC5
SOFTWARE
HIS D:54 , GLY D:55 , SER D:56 , TYR D:59 , LYS D:335
BINDING SITE FOR RESIDUE QV7 D 503
06
AC6
SOFTWARE
SER A:53 , HIS A:54 , GLY A:55 , LYS A:335 , HOH A:655 , ARG B:231 , ARG B:404 , ARG B:407 , QV7 B:499 , QV8 B:500
BINDING SITE FOR RESIDUE QV7 A 499
07
AC7
SOFTWARE
SER A:400 , ASN A:401 , THR A:402 , GLY A:403 , ARG A:404 , SER A:405
BINDING SITE FOR RESIDUE SO4 A 500
08
AC8
SOFTWARE
GLU A:240 , ASP A:264
BINDING SITE FOR RESIDUE K A 501
09
AC9
SOFTWARE
GLN A:354 , LEU A:357 , GLU A:359
BINDING SITE FOR RESIDUE K A 502
10
BC1
SOFTWARE
THR A:26 , PRO A:29 , ASN A:51 , HIS A:54 , GLY A:55 , SER A:56 , TYR A:59 , ALA A:334 , LYS A:335 , QV7 A:499 , THR B:402 , ARG B:404 , ASP B:482 , HIS B:483 , LYS B:486 , HOH B:514
BINDING SITE FOR RESIDUE QV7 B 499
11
BC2
SOFTWARE
QV7 A:499 , ARG B:231 , ASP B:232 , THR B:402 , ARG B:424
BINDING SITE FOR RESIDUE QV8 B 500
12
BC3
SOFTWARE
SER A:1 , SER B:1 , TYR B:360 , VAL B:361 , ASN B:364 , QV7 B:504 , ASN D:364 , LYS D:368 , HOH D:507
BINDING SITE FOR RESIDUE QV7 B 501
13
BC4
SOFTWARE
GLN B:354 , LEU B:357 , GLU B:359 , HOH B:575
BINDING SITE FOR RESIDUE K B 503
14
BC5
SOFTWARE
SER A:1 , TYR A:360 , VAL A:361 , ASN A:364 , SER B:1 , QV7 B:501 , SER C:1 , VAL C:361 , LYS C:368
BINDING SITE FOR RESIDUE QV7 B 504
15
BC6
SOFTWARE
SER C:400 , ASN C:401 , THR C:402 , ARG C:404 , SER C:405 , ALA C:481 , ASP C:482
BINDING SITE FOR RESIDUE SO4 C 499
16
BC7
SOFTWARE
ASN C:51 , SER C:53 , ASP C:83 , THR C:84 , LYS C:238 , HOH C:656
BINDING SITE FOR RESIDUE K C 500
17
BC8
SOFTWARE
GLN C:354 , LEU C:357 , GLU C:359
BINDING SITE FOR RESIDUE K C 501
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: PYRUVATE_KINASE (A:233-245,B:233-245,C:233-245,D:23...)
;
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
4
A:233-245
B:233-245
C:233-245
D:233-245
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(3, 10)
Info
All SCOP Domains
1a: SCOP_d3qv7a2 (A:88-186)
1b: SCOP_d3qv7d2 (D:88-186)
2a: SCOP_d3qv7a3 (A:358-498)
2b: SCOP_d3qv7b2 (B:358-498)
2c: SCOP_d3qv7c2 (C:358-498)
2d: SCOP_d3qv7d3 (D:358-498)
3a: SCOP_d3qv7a1 (A:1-87,A:187-357)
3b: SCOP_d3qv7b1 (B:1-87,B:187-357)
3c: SCOP_d3qv7c1 (C:1-87,C:187-357)
3d: SCOP_d3qv7d1 (D:1-87,D:187-357)
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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)
Trypanosome (Leishmania mexicana) [TaxId: 5665]
(11)
1a
d3qv7a2
A:88-186
1b
d3qv7d2
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
d3qv7a3
A:358-498
2b
d3qv7b2
B:358-498
2c
d3qv7c2
C:358-498
2d
d3qv7d3
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
d3qv7a1
A:1-87,A:187-357
3b
d3qv7b1
B:1-87,B:187-357
3c
d3qv7c1
C:1-87,C:187-357
3d
d3qv7d1
D:1-87,D:187-357
[
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Sorry, no Info available
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Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_PK_3qv7D01 (D:18-363)
1b: PFAM_PK_3qv7D02 (D:18-363)
1c: PFAM_PK_3qv7D03 (D:18-363)
1d: PFAM_PK_3qv7D04 (D:18-363)
2a: PFAM_PK_C_3qv7D05 (D:377-496)
2b: PFAM_PK_C_3qv7D06 (D:377-496)
2c: PFAM_PK_C_3qv7D07 (D:377-496)
2d: PFAM_PK_C_3qv7D08 (D:377-496)
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Clans
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(
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(
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(
)
Organisms
(
)
(
)
Clan
:
PK_TIM
(63)
Family
:
PK
(17)
Leishmania mexicana
(6)
1a
PK-3qv7D01
D:18-363
1b
PK-3qv7D02
D:18-363
1c
PK-3qv7D03
D:18-363
1d
PK-3qv7D04
D:18-363
Clan
:
no clan defined [family: PK_C]
(19)
Family
:
PK_C
(19)
Leishmania mexicana
(6)
2a
PK_C-3qv7D05
D:377-496
2b
PK_C-3qv7D06
D:377-496
2c
PK_C-3qv7D07
D:377-496
2d
PK_C-3qv7D08
D:377-496
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