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1J3J
Asym. Unit
Info
Asym.Unit (207 KB)
Biol.Unit 1 (201 KB)
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(1)
Title
:
DOUBLE MUTANT (C59R+S108N) PLASMODIUM FALCIPARUM DIHYDROFOLATE REDUCTASE-THYMIDYLATE SYNTHASE (PFDHFR-TS) COMPLEXED WITH PYRIMETHAMINE, NADPH, AND DUMP
Authors
:
J. Yuvaniyama, P. Chitnumsub, S. Kamchonwongpaisan, J. Vanichtanankul, W. Sirawaraporn, P. Taylor, M. Walkinshaw, Y. Yuthavong
Date
:
03 Feb 03 (Deposition) - 06 May 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Bifunctional, Oxidoreductase, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Yuvaniyama, P. Chitnumsub, S. Kamchonwongpaisan, J. Vanichtanankul, W. Sirawaraporn, P. Taylor, M. D. Walkinshaw, Y. Yuthavong
Insights Into Antifolate Resistance From Malarial Dhfr-Ts Structures.
Nat. Struct. Biol. V. 10 357 2003
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 6)
Info
All Hetero Components
1a: 5-(4-CHLORO-PHENYL)-6-ETHYL-PYRIMI... (CP6a)
1b: 5-(4-CHLORO-PHENYL)-6-ETHYL-PYRIMI... (CP6b)
2a: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPa)
2b: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPb)
3a: 2'-DEOXYURIDINE 5'-MONOPHOSPHATE (UMPa)
3b: 2'-DEOXYURIDINE 5'-MONOPHOSPHATE (UMPb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CP6
2
Ligand/Ion
5-(4-CHLORO-PHENYL)-6-ETHYL-PYRIMIDINE-2,4-DIAMINE
2
NDP
2
Ligand/Ion
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
3
UMP
2
Ligand/Ion
2'-DEOXYURIDINE 5'-MONOPHOSPHATE
[
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Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ILE A:14 , CYS A:15 , ASP A:54 , PHE A:58 , ASN A:108 , SER A:111 , ILE A:112 , ILE A:164 , TYR A:170 , THR A:185 , NDP A:610
BINDING SITE FOR RESIDUE CP6 A 609
2
AC2
SOFTWARE
CYS A:15 , ALA A:16 , LEU A:40 , GLY A:44 , VAL A:45 , LEU A:46 , TRP A:48 , GLY A:105 , ARG A:106 , THR A:107 , ASN A:108 , LEU A:127 , SER A:128 , ARG A:129 , THR A:130 , ASN A:144 , ILE A:164 , GLY A:165 , GLY A:166 , SER A:167 , VAL A:168 , VAL A:169 , TYR A:170 , GLU A:172 , VAL A:195 , CP6 A:609 , HOH A:1424 , HOH A:1425 , HOH A:1426 , HOH A:1427
BINDING SITE FOR RESIDUE NDP A 610
3
AC3
SOFTWARE
CYS C:490 , HIS C:491 , GLN C:509 , ARG C:510 , SER C:511 , ASP C:513 , GLY C:517 , ASN C:521 , HIS C:551 , TYR C:553 , HOH C:1183 , HOH C:1375 , ARG D:470 , ARG D:471
BINDING SITE FOR RESIDUE UMP C 611
4
AC4
SOFTWARE
ILE B:14 , CYS B:15 , ALA B:16 , ASP B:54 , PHE B:58 , ASN B:108 , SER B:111 , ILE B:112 , ILE B:164 , TYR B:170 , THR B:185 , NDP B:710
BINDING SITE FOR RESIDUE CP6 B 709
5
AC5
SOFTWARE
CYS B:15 , ALA B:16 , LEU B:40 , GLY B:44 , VAL B:45 , GLY B:105 , ARG B:106 , THR B:107 , ASN B:108 , LEU B:127 , SER B:128 , ARG B:129 , THR B:130 , ASN B:144 , LYS B:145 , ILE B:164 , GLY B:165 , GLY B:166 , SER B:167 , VAL B:168 , VAL B:169 , TYR B:170 , GLU B:172 , VAL B:195 , CP6 B:709 , HOH B:1627
BINDING SITE FOR RESIDUE NDP B 710
6
AC6
SOFTWARE
ARG C:470 , ARG C:471 , CYS D:490 , HIS D:491 , GLN D:509 , ARG D:510 , SER D:511 , ASP D:513 , ASN D:521 , HIS D:551 , TYR D:553 , HOH D:1073
BINDING SITE FOR RESIDUE UMP D 711
[
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SAPs(SNPs)/Variants
(4, 8)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_DRTS_PLAFK_001 (A16V, chain A/B, )
2: VAR_DRTS_PLAFK_002 (N51I, chain A/B, )
3: VAR_DRTS_PLAFK_003 (R59C, chain A/B, )
4: VAR_DRTS_PLAFK_004 (N108T, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_DRTS_PLAFK_001
*
A
16
V
DRTS_PLAFK
---
---
A/B
A
16
V
2
UniProt
VAR_DRTS_PLAFK_002
*
N
51
I
DRTS_PLAFK
---
---
A/B
N
51
I
3
UniProt
VAR_DRTS_PLAFK_003
*
R
59
C
DRTS_PLAFK
---
---
A/B
R
59
C
4
UniProt
VAR_DRTS_PLAFK_004
*
N
108
T
DRTS_PLAFK
---
---
A/B
N
108
T
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 6)
Info
All PROSITE Patterns/Profiles
1: DHFR_2 (A:10-228,B:10-228)
2: DHFR_1 (A:39-62,B:39-62)
3: THYMIDYLATE_SYNTHASE (C:470-498,D:470-498)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DHFR_2
PS51330
Dihydrofolate reductase (DHFR) domain profile.
DRTS_PLAFK
10-228
2
A:10-228
B:10-228
2
DHFR_1
PS00075
Dihydrofolate reductase (DHFR) domain signature.
DRTS_PLAFK
39-62
2
A:39-62
B:39-62
3
THYMIDYLATE_SYNTHASE
PS00091
Thymidylate synthase active site.
DRTS_PLAFK
470-498
2
C:470-498
D:470-498
[
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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.
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1j3jc_ (C:)
1b: SCOP_d1j3jd_ (D:)
2a: SCOP_d1j3ja_ (A:)
2b: SCOP_d1j3jb_ (B:)
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)
Protein Domains
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(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Thymidylate synthase/dCMP hydroxymethylase
(193)
Superfamily
:
Thymidylate synthase/dCMP hydroxymethylase
(193)
Family
:
Thymidylate synthase/dCMP hydroxymethylase
(183)
Protein domain
:
Bifunctional enzyme dihydrofolate reductase-thymidylate synthase, TS domain
(5)
Malaria parasite (Plasmodium falciparum) [TaxId: 5833]
(3)
1a
d1j3jc_
C:
1b
d1j3jd_
D:
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Dihydrofolate reductase-like
(332)
Superfamily
:
Dihydrofolate reductase-like
(332)
Family
:
Dihydrofolate reductases
(249)
Protein domain
:
Bifunctional enzyme dihydrofolate reductase-thymidylate synthase, DFR domain
(7)
Malaria parasite (Plasmodium falciparum) [TaxId: 5833]
(5)
2a
d1j3ja_
A:
2b
d1j3jb_
B:
[
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]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1j3jC00 (C:283-608)
1b: CATH_1j3jD00 (D:283-608)
2a: CATH_1j3jB00 (B:1-231)
2b: CATH_1j3jA00 (A:1-231)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Thymidylate Synthase; Chain A
(160)
Homologous Superfamily
:
Thymidylate Synthase, chain A
(160)
Malaria parasite p (Plasmodium falciparum)
(3)
1a
1j3jC00
C:283-608
1b
1j3jD00
D:283-608
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Dihydrofolate Reductase, subunit A
(200)
Homologous Superfamily
:
Dihydrofolate Reductase, subunit A
(200)
Malaria parasite p (Plasmodium falciparum)
(3)
2a
1j3jB00
B:1-231
2b
1j3jA00
A:1-231
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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