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1PZF
Asym. Unit
Info
Asym.Unit (217 KB)
Biol.Unit 1 (211 KB)
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(1)
Title
:
T.GONDII LDH1 TERNARY COMPLEX WITH APAD+ AND OXALATE
Authors
:
K. L. Kavanagh, R. A. Elling, D. K. Wilson
Date
:
10 Jul 03 (Deposition) - 24 Feb 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Apad, Rossmann Fold, Tetramer, Apicomplexa, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. L. Kavanagh, R. A. Elling, D. K. Wilson
Structure Of Toxoplasma Gondii Ldh1: Active-Site Differences From Human Lactate Dehydrogenases And The Structural Basis For Efficient Apad+ Use.
Biochemistry V. 43 879 2004
(for further references see the
PDB file header
)
[
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Hetero Components
(2, 8)
Info
All Hetero Components
1a: 3-ACETYLPYRIDINE ADENINE DINUCLEOT... (A3Da)
1b: 3-ACETYLPYRIDINE ADENINE DINUCLEOT... (A3Db)
1c: 3-ACETYLPYRIDINE ADENINE DINUCLEOT... (A3Dc)
1d: 3-ACETYLPYRIDINE ADENINE DINUCLEOT... (A3Dd)
2a: OXALATE ION (OXLa)
2b: OXALATE ION (OXLb)
2c: OXALATE ION (OXLc)
2d: OXALATE ION (OXLd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
A3D
4
Ligand/Ion
3-ACETYLPYRIDINE ADENINE DINUCLEOTIDE
2
OXL
4
Ligand/Ion
OXALATE ION
[
close Hetero Component info
]
Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
TRP A:107 , ARG A:109 , ASN A:140 , ARG A:171 , HIS A:195 , GLY A:236 , A3D A:401 , HOH A:404 , HOH A:492
BINDING SITE FOR RESIDUE OXL A 402
2
AC2
SOFTWARE
TRP B:107 , ARG B:109 , ASN B:140 , ARG B:171 , HIS B:195 , A3D B:403 , HOH B:412
BINDING SITE FOR RESIDUE OXL B 404
3
AC3
SOFTWARE
TRP C:107 , ARG C:109 , ASN C:140 , ARG C:171 , HIS C:195 , GLY C:236 , ALA C:246 , A3D C:405 , HOH C:410
BINDING SITE FOR RESIDUE OXL C 406
4
AC4
SOFTWARE
TRP D:107 , ARG D:109 , ASN D:140 , ARG D:171 , HIS D:195 , GLY D:236 , A3D D:407 , HOH D:432 , HOH D:452
BINDING SITE FOR RESIDUE OXL D 408
5
AC5
SOFTWARE
GLY A:29 , MET A:30 , ILE A:31 , TYR A:52 , ASP A:53 , VAL A:54 , VAL A:55 , MET A:58 , THR A:97 , ALA A:98 , GLY A:99 , LEU A:100 , THR A:101 , ILE A:119 , VAL A:138 , ASN A:140 , LEU A:142 , MET A:163 , LEU A:167 , HIS A:195 , ALA A:246 , OXL A:402 , HOH A:404 , HOH A:405 , HOH A:407 , HOH A:466 , HOH A:475 , HOH A:495 , HOH A:504
BINDING SITE FOR RESIDUE A3D A 401
6
AC6
SOFTWARE
GLY B:29 , MET B:30 , ILE B:31 , TYR B:52 , ASP B:53 , VAL B:54 , VAL B:55 , MET B:58 , THR B:97 , ALA B:98 , GLY B:99 , LEU B:100 , THR B:101 , ILE B:119 , VAL B:138 , THR B:139 , ASN B:140 , LEU B:142 , MET B:163 , LEU B:167 , HIS B:195 , ALA B:246 , OXL B:404 , HOH B:405 , HOH B:419 , HOH B:424 , HOH B:433 , HOH B:482
BINDING SITE FOR RESIDUE A3D B 403
7
AC7
SOFTWARE
GLY C:29 , MET C:30 , ILE C:31 , TYR C:52 , ASP C:53 , VAL C:54 , VAL C:55 , MET C:58 , THR C:97 , ALA C:98 , GLY C:99 , LEU C:100 , THR C:101 , ILE C:119 , VAL C:138 , THR C:139 , ASN C:140 , MET C:163 , LEU C:167 , HIS C:195 , ALA C:246 , OXL C:406 , HOH C:407 , HOH C:408 , HOH C:489
BINDING SITE FOR RESIDUE A3D C 405
8
AC8
SOFTWARE
GLY D:29 , MET D:30 , ILE D:31 , TYR D:52 , ASP D:53 , VAL D:54 , VAL D:55 , MET D:58 , THR D:97 , ALA D:98 , GLY D:99 , LEU D:100 , THR D:101 , ILE D:119 , VAL D:138 , THR D:139 , ASN D:140 , MET D:163 , LEU D:167 , HIS D:195 , ALA D:246 , OXL D:408 , HOH D:411 , HOH D:437 , HOH D:452 , HOH D:462
BINDING SITE FOR RESIDUE A3D D 407
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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End label:
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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
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1pzfa2 (A:164-334)
1b: SCOP_d1pzfb2 (B:164-334)
1c: SCOP_d1pzfc2 (C:164-332)
1d: SCOP_d1pzfd2 (D:164-332)
2a: SCOP_d1pzfa1 (A:14-163)
2b: SCOP_d1pzfb1 (B:14-163)
2c: SCOP_d1pzfc1 (C:14-163)
2d: SCOP_d1pzfd1 (D:14-163)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
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(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
LDH C-terminal domain-like
(172)
Superfamily
:
LDH C-terminal domain-like
(172)
Family
:
Lactate & malate dehydrogenases, C-terminal domain
(125)
Protein domain
:
Lactate dehydrogenase
(55)
Toxoplasma gondii [TaxId: 5811]
(5)
1a
d1pzfa2
A:164-334
1b
d1pzfb2
B:164-334
1c
d1pzfc2
C:164-332
1d
d1pzfd2
D:164-332
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
LDH N-terminal domain-like
(117)
Protein domain
:
Lactate dehydrogenase
(53)
Toxoplasma gondii [TaxId: 5811]
(5)
2a
d1pzfa1
A:14-163
2b
d1pzfb1
B:14-163
2c
d1pzfc1
C:14-163
2d
d1pzfd1
D:14-163
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1pzfA01 (A:14-162)
1b: CATH_1pzfB01 (B:14-162)
1c: CATH_1pzfC01 (C:14-162)
1d: CATH_1pzfD01 (D:14-162)
2a: CATH_1pzfC02 (C:163-332)
2b: CATH_1pzfD02 (D:163-332)
2c: CATH_1pzfA02 (A:163-334)
2d: CATH_1pzfB02 (B:163-334)
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)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Toxoplasma gondii. Organism_taxid: 5811.
(2)
1a
1pzfA01
A:14-162
1b
1pzfB01
B:14-162
1c
1pzfC01
C:14-162
1d
1pzfD01
D:14-162
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2
(116)
Homologous Superfamily
:
L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2
(116)
Toxoplasma gondii. Organism_taxid: 5811.
(2)
2a
1pzfC02
C:163-332
2b
1pzfD02
D:163-332
2c
1pzfA02
A:163-334
2d
1pzfB02
B:163-334
[
close CATH info
]
Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_Ldh_1_C_1pzfD01 (D:165-331)
1b: PFAM_Ldh_1_C_1pzfD02 (D:165-331)
1c: PFAM_Ldh_1_C_1pzfD03 (D:165-331)
1d: PFAM_Ldh_1_C_1pzfD04 (D:165-331)
2a: PFAM_Ldh_1_N_1pzfD05 (D:21-162)
2b: PFAM_Ldh_1_N_1pzfD06 (D:21-162)
2c: PFAM_Ldh_1_N_1pzfD07 (D:21-162)
2d: PFAM_Ldh_1_N_1pzfD08 (D:21-162)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
LDH_C
(56)
Family
:
Ldh_1_C
(51)
Toxoplasma gondii
(7)
1a
Ldh_1_C-1pzfD01
D:165-331
1b
Ldh_1_C-1pzfD02
D:165-331
1c
Ldh_1_C-1pzfD03
D:165-331
1d
Ldh_1_C-1pzfD04
D:165-331
Clan
:
NADP_Rossmann
(1239)
Family
:
Ldh_1_N
(51)
Toxoplasma gondii
(7)
2a
Ldh_1_N-1pzfD05
D:21-162
2b
Ldh_1_N-1pzfD06
D:21-162
2c
Ldh_1_N-1pzfD07
D:21-162
2d
Ldh_1_N-1pzfD08
D:21-162
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