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1PKL
Asym. Unit
Info
Asym.Unit (626 KB)
Biol.Unit 1 (311 KB)
Biol.Unit 2 (316 KB)
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(1)
Title
:
THE STRUCTURE OF LEISHMANIA PYRUVATE KINASE
Authors
:
D. J. Rigden, S. E. V. Phillips, P. A. M. Michels, L. A. Fothergill-Gilmo
Date
:
15 Sep 98 (Deposition) - 23 Sep 98 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.35
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
:
Pyruvate Kinase, Glycolytic Enzyme, Homotetramer, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. J. Rigden, S. E. Phillips, P. A. Michels, L. A. Fothergill-Gilmore
The Structure Of Pyruvate Kinase From Leishmania Mexicana Reveals Details Of The Allosteric Transition And Unusual Effector Specificity.
J. Mol. Biol. V. 291 615 1999
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Hetero Components
(1, 8)
Info
All Hetero Components
1a: SULFATE ION (SO4a)
1b: SULFATE ION (SO4b)
1c: SULFATE ION (SO4c)
1d: SULFATE ION (SO4d)
1e: SULFATE ION (SO4e)
1f: SULFATE ION (SO4f)
1g: SULFATE ION (SO4g)
1h: SULFATE ION (SO4h)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
SO4
8
Ligand/Ion
SULFATE ION
[
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Sites
(13, 13)
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: ADP (AUTHOR)
10: ALL (AUTHOR)
11: DIV (AUTHOR)
12: MON (AUTHOR)
13: PEP (AUTHOR)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER A:400 , ASN A:401 , THR A:402 , ARG A:404 , SER A:405 , HOH A:3237
BINDING SITE FOR RESIDUE SO4 A 3000
02
AC2
SOFTWARE
SER B:400 , ASN B:401 , THR B:402 , GLY B:403 , ARG B:404 , SER B:405
BINDING SITE FOR RESIDUE SO4 B 3001
03
AC3
SOFTWARE
SER C:400 , ASN C:401 , THR C:402 , ARG C:404 , SER C:405 , ALA C:481
BINDING SITE FOR RESIDUE SO4 C 3002
04
AC4
SOFTWARE
SER D:400 , ASN D:401 , THR D:402 , GLY D:403 , ARG D:404 , SER D:405
BINDING SITE FOR RESIDUE SO4 D 3003
05
AC5
SOFTWARE
SER E:400 , ASN E:401 , THR E:402 , ARG E:404 , SER E:405 , ALA E:481 , HOH E:1541
BINDING SITE FOR RESIDUE SO4 E 3004
06
AC6
SOFTWARE
SER F:400 , ASN F:401 , THR F:402 , ARG F:404 , SER F:405
BINDING SITE FOR RESIDUE SO4 F 3005
07
AC7
SOFTWARE
SER H:400 , ASN H:401 , THR H:402 , GLY H:403 , ARG H:404 , SER H:405 , ALA H:481
BINDING SITE FOR RESIDUE SO4 H 3006
08
AC8
SOFTWARE
SER G:400 , THR G:402 , ARG G:404 , SER G:405 , ALA G:481 , ASP G:482 , HOH G:2654 , HOH G:2773 , HOH G:2900
BINDING SITE FOR RESIDUE SO4 G 3007
09
ADP
AUTHOR
ARG A:49 , ASN A:51 , HIS A:54 , ARG A:90 , ARG A:174
ADP SUBSTRATE BINDING SITE, BY ANALOGY WITH OTHER CRYSTAL STRUCTURES
10
ALL
AUTHOR
SER A:400 , THR A:402 , ARG A:404 , SER A:405 , LYS A:453 , ARG A:456 , HIS A:480
PUTATIVE ALLOSTERIC EFFECTOR SITE, PARTLY BY ANALOGY WITH OTHER CRYSTAL STRUCTURES
11
DIV
AUTHOR
GLU A:240 , ASP A:264
DIVALENT CATION BINDING SITE, BY ANALOGY WITH OTHER CRYSTAL STRUCTURES
12
MON
AUTHOR
ASN A:51 , SER A:53 , ASP A:83 , THR A:84
MONOVALENT CATION BINDING SITE, BY ANALOGY WITH OTHER CRYSTAL STRUCTURES
13
PEP
AUTHOR
ARG A:49 , ARG A:90 , LYS A:238 , THR A:296
PEP SUBSTRATE BINDING SITE, BY ANALOGY WITH OTHER CRYSTAL STRUCTURES
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 8)
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
8
A:233-245
B:233-245
C:233-245
D:233-245
E:233-245
F:233-245
G:233-245
H:233-245
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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.
SCOP Domains
(3, 24)
Info
All SCOP Domains
1a: SCOP_d1pkla1 (A:88-186)
1b: SCOP_d1pklb1 (B:88-186)
1c: SCOP_d1pklc1 (C:88-186)
1d: SCOP_d1pkld1 (D:88-186)
1e: SCOP_d1pkle1 (E:88-186)
1f: SCOP_d1pklf1 (F:88-186)
1g: SCOP_d1pklg1 (G:88-186)
1h: SCOP_d1pklh1 (H:88-186)
2a: SCOP_d1pkla3 (A:358-498)
2b: SCOP_d1pklb3 (B:358-498)
2c: SCOP_d1pklc3 (C:358-498)
2d: SCOP_d1pkld3 (D:358-498)
2e: SCOP_d1pkle3 (E:358-498)
2f: SCOP_d1pklf3 (F:358-498)
2g: SCOP_d1pklg3 (G:358-498)
2h: SCOP_d1pklh3 (H:358-498)
3a: SCOP_d1pkla2 (A:1-87,A:187-357)
3b: SCOP_d1pklb2 (B:1-87,B:187-357)
3c: SCOP_d1pklc2 (C:1-87,C:187-357)
3d: SCOP_d1pkld2 (D:1-87,D:187-357)
3e: SCOP_d1pkle2 (E:1-87,E:187-357)
3f: SCOP_d1pklf2 (F:1-87,F:187-357)
3g: SCOP_d1pklg2 (G:1-87,G:187-357)
3h: SCOP_d1pklh2 (H:1-87,H:187-357)
View:
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Classes
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)
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)
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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
d1pkla1
A:88-186
1b
d1pklb1
B:88-186
1c
d1pklc1
C:88-186
1d
d1pkld1
D:88-186
1e
d1pkle1
E:88-186
1f
d1pklf1
F:88-186
1g
d1pklg1
G:88-186
1h
d1pklh1
H: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
d1pkla3
A:358-498
2b
d1pklb3
B:358-498
2c
d1pklc3
C:358-498
2d
d1pkld3
D:358-498
2e
d1pkle3
E:358-498
2f
d1pklf3
F:358-498
2g
d1pklg3
G:358-498
2h
d1pklh3
H: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
d1pkla2
A:1-87,A:187-357
3b
d1pklb2
B:1-87,B:187-357
3c
d1pklc2
C:1-87,C:187-357
3d
d1pkld2
D:1-87,D:187-357
3e
d1pkle2
E:1-87,E:187-357
3f
d1pklf2
F:1-87,F:187-357
3g
d1pklg2
G:1-87,G:187-357
3h
d1pklh2
H:1-87,H:187-357
[
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]
CATH Domains
(3, 24)
Info
all CATH domains
1a: CATH_1pklG01 (G:1-18,G:354-498)
1b: CATH_1pklD01 (D:1-18,D:354-497)
1c: CATH_1pklE01 (E:1-18,E:354-497)
1d: CATH_1pklC01 (C:1-18,C:354-497)
1e: CATH_1pklH01 (H:1-18,H:354-497)
1f: CATH_1pklA01 (A:1-18,A:354-497)
1g: CATH_1pklF01 (F:1-18,F:354-497)
1h: CATH_1pklB01 (B:1-18,B:354-497)
2a: CATH_1pklA02 (A:19-86,A:188-353)
2b: CATH_1pklB02 (B:19-86,B:188-353)
2c: CATH_1pklC02 (C:19-86,C:188-353)
2d: CATH_1pklD02 (D:19-86,D:188-353)
2e: CATH_1pklE02 (E:19-86,E:188-353)
2f: CATH_1pklF02 (F:19-86,F:188-353)
2g: CATH_1pklG02 (G:19-86,G:188-353)
2h: CATH_1pklH02 (H:19-86,H:188-353)
3a: CATH_1pklA03 (A:87-187)
3b: CATH_1pklB03 (B:87-187)
3c: CATH_1pklC03 (C:87-187)
3d: CATH_1pklD03 (D:87-187)
3e: CATH_1pklE03 (E:87-187)
3f: CATH_1pklF03 (F:87-187)
3g: CATH_1pklG03 (G:87-187)
3h: CATH_1pklH03 (H:87-187)
View:
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)
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(
)
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)
Leishmania mexicana. Organism_taxid: 5665. Strain: mhom/bz/84/bel46.
(1)
1a
1pklG01
G:1-18,G:354-498
1b
1pklD01
D:1-18,D:354-497
1c
1pklE01
E:1-18,E:354-497
1d
1pklC01
C:1-18,C:354-497
1e
1pklH01
H:1-18,H:354-497
1f
1pklA01
A:1-18,A:354-497
1g
1pklF01
F:1-18,F:354-497
1h
1pklB01
B:1-18,B:354-497
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Phosphoenolpyruvate-binding domains
(67)
Leishmania mexicana. Organism_taxid: 5665. Strain: mhom/bz/84/bel46.
(1)
2a
1pklA02
A:19-86,A:188-353
2b
1pklB02
B:19-86,B:188-353
2c
1pklC02
C:19-86,C:188-353
2d
1pklD02
D:19-86,D:188-353
2e
1pklE02
E:19-86,E:188-353
2f
1pklF02
F:19-86,F:188-353
2g
1pklG02
G:19-86,G:188-353
2h
1pklH02
H:19-86,H:188-353
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
M1 Pyruvate Kinase; Domain 3
(24)
Homologous Superfamily
:
M1 Pyruvate Kinase; Domain 3
(20)
Leishmania mexicana. Organism_taxid: 5665. Strain: mhom/bz/84/bel46.
(1)
3a
1pklA03
A:87-187
3b
1pklB03
B:87-187
3c
1pklC03
C:87-187
3d
1pklD03
D:87-187
3e
1pklE03
E:87-187
3f
1pklF03
F:87-187
3g
1pklG03
G:87-187
3h
1pklH03
H:87-187
[
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Pfam Domains
(2, 16)
Info
all PFAM domains
1a: PFAM_PK_1pklH01 (H:18-363)
1b: PFAM_PK_1pklH02 (H:18-363)
1c: PFAM_PK_1pklH03 (H:18-363)
1d: PFAM_PK_1pklH04 (H:18-363)
1e: PFAM_PK_1pklH05 (H:18-363)
1f: PFAM_PK_1pklH06 (H:18-363)
1g: PFAM_PK_1pklH07 (H:18-363)
1h: PFAM_PK_1pklH08 (H:18-363)
2a: PFAM_PK_C_1pklH09 (H:377-496)
2b: PFAM_PK_C_1pklH10 (H:377-496)
2c: PFAM_PK_C_1pklH11 (H:377-496)
2d: PFAM_PK_C_1pklH12 (H:377-496)
2e: PFAM_PK_C_1pklH13 (H:377-496)
2f: PFAM_PK_C_1pklH14 (H:377-496)
2g: PFAM_PK_C_1pklH15 (H:377-496)
2h: PFAM_PK_C_1pklH16 (H:377-496)
View:
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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-1pklH01
H:18-363
1b
PK-1pklH02
H:18-363
1c
PK-1pklH03
H:18-363
1d
PK-1pklH04
H:18-363
1e
PK-1pklH05
H:18-363
1f
PK-1pklH06
H:18-363
1g
PK-1pklH07
H:18-363
1h
PK-1pklH08
H:18-363
Clan
:
no clan defined [family: PK_C]
(19)
Family
:
PK_C
(19)
Leishmania mexicana
(6)
2a
PK_C-1pklH09
H:377-496
2b
PK_C-1pklH10
H:377-496
2c
PK_C-1pklH11
H:377-496
2d
PK_C-1pklH12
H:377-496
2e
PK_C-1pklH13
H:377-496
2f
PK_C-1pklH14
H:377-496
2g
PK_C-1pklH15
H:377-496
2h
PK_C-1pklH16
H:377-496
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