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3E0V
Biol. Unit 1
Info
Asym.Unit (479 KB)
Biol.Unit 1 (313 KB)
Biol.Unit 2 (313 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF PYRUVATE KINASE FROM LEISHMANIA MEXICANA IN COMPLEX WITH SULPHATE IONS
Authors
:
L. B. Tulloch, L. A. Gillmore, M. D. Walkinshaw
Date
:
01 Aug 08 (Deposition) - 19 Aug 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.30
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F (2x)
Keywords
:
Pyruvate, Kinase, Nad+ Nadh, Adp, Phosphoenolpyruvate, Pep, Glycolysis, Trypanosomatid, Leishmania, Mexicana, Allosteric Enzyme, Magnesium, Metal-Binding, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. B. Tulloch, H. P. Morgan, V. Hannaert, P. A. Michels, L. A. Fothergill-Gilmore, M. D. Walkinshaw
Sulphate Removal Induces A Major Conformational Change In Leishmania Mexicana Pyruvate Kinase In The Crystalline State.
J. Mol. Biol. V. 383 615 2008
[
close entry info
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Hetero Components
(2, 30)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
2a: SULFATE ION (SO4a)
2aa: SULFATE ION (SO4aa)
2ab: SULFATE ION (SO4ab)
2ac: SULFATE ION (SO4ac)
2ad: SULFATE ION (SO4ad)
2ae: SULFATE ION (SO4ae)
2af: SULFATE ION (SO4af)
2ag: SULFATE ION (SO4ag)
2ah: SULFATE ION (SO4ah)
2ai: SULFATE ION (SO4ai)
2aj: SULFATE ION (SO4aj)
2ak: SULFATE ION (SO4ak)
2al: SULFATE ION (SO4al)
2am: SULFATE ION (SO4am)
2an: SULFATE ION (SO4an)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
2e: SULFATE ION (SO4e)
2f: SULFATE ION (SO4f)
2g: SULFATE ION (SO4g)
2h: SULFATE ION (SO4h)
2i: SULFATE ION (SO4i)
2j: SULFATE ION (SO4j)
2k: SULFATE ION (SO4k)
2l: SULFATE ION (SO4l)
2m: SULFATE ION (SO4m)
2n: SULFATE ION (SO4n)
2o: SULFATE ION (SO4o)
2p: SULFATE ION (SO4p)
2q: SULFATE ION (SO4q)
2r: SULFATE ION (SO4r)
2s: SULFATE ION (SO4s)
2t: SULFATE ION (SO4t)
2u: SULFATE ION (SO4u)
2v: SULFATE ION (SO4v)
2w: SULFATE ION (SO4w)
2x: SULFATE ION (SO4x)
2y: SULFATE ION (SO4y)
2z: SULFATE ION (SO4z)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
2
Ligand/Ion
GLYCEROL
2
SO4
28
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(31, 31)
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: EC5 (SOFTWARE)
30: EC6 (SOFTWARE)
31: EC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:49 , ASN A:51 , LYS A:238
BINDING SITE FOR RESIDUE SO4 A 501
02
AC2
SOFTWARE
GLN A:297 , GLU A:300 , SER A:330 , GLY A:331 , GLU A:332
BINDING SITE FOR RESIDUE SO4 A 502
03
AC3
SOFTWARE
HIS A:54 , ARG A:174
BINDING SITE FOR RESIDUE SO4 A 503
04
AC4
SOFTWARE
HIS A:54 , ARG A:90 , ARG A:175
BINDING SITE FOR RESIDUE SO4 A 506
05
AC5
SOFTWARE
SER A:400 , ASN A:401 , THR A:402 , GLY A:403 , ARG A:404 , SER A:405 , ALA A:481 , ASP A:482
BINDING SITE FOR RESIDUE SO4 A 507
06
AC6
SOFTWARE
LYS A:453 , ARG A:456
BINDING SITE FOR RESIDUE SO4 A 508
07
AC7
SOFTWARE
SER A:1 , GLN A:2 , GLN B:2 , HOH B:1113
BINDING SITE FOR RESIDUE SO4 B 504
08
AC8
SOFTWARE
ARG B:49 , ASN B:51 , SER B:53 , LYS B:238
BINDING SITE FOR RESIDUE SO4 B 501
09
AC9
SOFTWARE
GLN B:297 , GLU B:300 , GLY B:331 , GLU B:332
BINDING SITE FOR RESIDUE SO4 B 502
10
BC1
SOFTWARE
SER B:53 , HIS B:54 , ARG B:174 , HOH B:1100
BINDING SITE FOR RESIDUE SO4 B 503
11
BC2
SOFTWARE
ASN B:178 , LEU B:179 , PRO B:180 , VAL B:184 , GLU B:268
BINDING SITE FOR RESIDUE SO4 B 505
12
BC3
SOFTWARE
HIS B:54 , ARG B:90 , ARG B:175 , LYS B:335
BINDING SITE FOR RESIDUE SO4 B 506
13
BC4
SOFTWARE
SER B:400 , ASN B:401 , THR B:402 , GLY B:403 , ARG B:404 , SER B:405 , ALA B:481 , ASP B:482
BINDING SITE FOR RESIDUE SO4 B 507
14
BC5
SOFTWARE
ARG B:456
BINDING SITE FOR RESIDUE SO4 B 508
15
BC6
SOFTWARE
ARG C:49 , ASN C:51 , LYS C:238
BINDING SITE FOR RESIDUE SO4 C 501
16
BC7
SOFTWARE
GLN C:297 , GLU C:300 , GLY C:331 , GLU C:332
BINDING SITE FOR RESIDUE SO4 C 502
17
BC8
SOFTWARE
SER C:53 , HIS C:54 , GLY C:55 , ARG C:174
BINDING SITE FOR RESIDUE SO4 C 503
18
BC9
SOFTWARE
ASN C:178 , LEU C:179 , VAL C:184 , ARG C:214 , GLN C:243 , GLU C:268
BINDING SITE FOR RESIDUE SO4 C 505
19
CC1
SOFTWARE
HIS C:54 , ARG C:90 , ARG C:175
BINDING SITE FOR RESIDUE SO4 C 506
20
CC2
SOFTWARE
SER C:400 , ASN C:401 , THR C:402 , GLY C:403 , ARG C:404 , SER C:405 , ALA C:481 , ASP C:482
BINDING SITE FOR RESIDUE SO4 C 507
21
CC3
SOFTWARE
ASN C:401 , ARG C:456
BINDING SITE FOR RESIDUE SO4 C 508
22
CC4
SOFTWARE
GLN C:2 , GLN D:2 , HOH D:2149
BINDING SITE FOR RESIDUE SO4 D 504
23
CC5
SOFTWARE
ARG D:49 , ASN D:51 , SER D:53 , LYS D:238
BINDING SITE FOR RESIDUE SO4 D 501
24
CC6
SOFTWARE
GLN D:297 , GLU D:300 , SER D:330 , GLY D:331 , GLU D:332
BINDING SITE FOR RESIDUE SO4 D 502
25
CC7
SOFTWARE
HIS D:54 , GLY D:55 , HOH D:2132
BINDING SITE FOR RESIDUE SO4 D 503
26
CC8
SOFTWARE
ASN D:178 , ASN D:241 , GLN D:243 , GLU D:268
BINDING SITE FOR RESIDUE SO4 D 505
27
CC9
SOFTWARE
HIS D:54 , ARG D:90 , ARG D:175 , LYS D:335
BINDING SITE FOR RESIDUE SO4 D 506
28
DC1
SOFTWARE
SER D:400 , ASN D:401 , THR D:402 , GLY D:403 , ARG D:404 , SER D:405 , ALA D:481 , ASP D:482
BINDING SITE FOR RESIDUE SO4 D 507
29
EC5
SOFTWARE
SER A:56 , LYS D:123 , GLU D:156
BINDING SITE FOR RESIDUE GOL A 509
30
EC6
SOFTWARE
ASN A:178 , LEU A:179 , CYS A:182 , VAL A:184 , ARG A:214 , GLN A:243 , GLU A:268
BINDING SITE FOR RESIDUE GOL A 510
31
EC7
SOFTWARE
PHE A:115 , LYS A:123 , GLY E:55 , SER E:56 , HOH E:3046 , HOH E:4110
BINDING SITE FOR RESIDUE GOL E 508
[
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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, 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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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, 18)
Info
All SCOP Domains
1a: SCOP_d3e0va1 (A:88-186)
1b: SCOP_d3e0vb1 (B:88-186)
1c: SCOP_d3e0vc1 (C:88-186)
1d: SCOP_d3e0vd1 (D:88-186)
1e: SCOP_d3e0ve1 (E:88-186)
1f: SCOP_d3e0vf1 (F:88-186)
2a: SCOP_d3e0va3 (A:358-498)
2b: SCOP_d3e0vb3 (B:358-498)
2c: SCOP_d3e0vc3 (C:358-498)
2d: SCOP_d3e0vd3 (D:358-498)
2e: SCOP_d3e0ve3 (E:358-498)
2f: SCOP_d3e0vf3 (F:358-498)
3a: SCOP_d3e0va2 (A:1-87,A:187-357)
3b: SCOP_d3e0vb2 (B:1-87,B:187-357)
3c: SCOP_d3e0vc2 (C:1-87,C:187-357)
3d: SCOP_d3e0vd2 (D:1-87,D:187-357)
3e: SCOP_d3e0ve2 (E:1-87,E:187-357)
3f: SCOP_d3e0vf2 (F:1-87,F:187-357)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
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)
Trypanosome (Leishmania mexicana) [TaxId: 5665]
(11)
1a
d3e0va1
A:88-186
1b
d3e0vb1
B:88-186
1c
d3e0vc1
C:88-186
1d
d3e0vd1
D:88-186
1e
d3e0ve1
E:88-186
1f
d3e0vf1
F: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
d3e0va3
A:358-498
2b
d3e0vb3
B:358-498
2c
d3e0vc3
C:358-498
2d
d3e0vd3
D:358-498
2e
d3e0ve3
E:358-498
2f
d3e0vf3
F: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
d3e0va2
A:1-87,A:187-357
3b
d3e0vb2
B:1-87,B:187-357
3c
d3e0vc2
C:1-87,C:187-357
3d
d3e0vd2
D:1-87,D:187-357
3e
d3e0ve2
E:1-87,E:187-357
3f
d3e0vf2
F:1-87,F:187-357
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
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Pfam Domains
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