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2P1D
Biol. Unit 1
Info
Asym.Unit (50 KB)
Biol.Unit 1 (45 KB)
Biol.Unit 2 (88 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF DENGUE METHYLTRANSFERASE IN COMPLEX WITH GTP AND S-ADENOSYL-L-HOMOCYSTEINE
Authors
:
M. P. Egloff, D. Benarooch, Marseilles Structural Genomics Progra (Msgp)
Date
:
05 Mar 07 (Deposition) - 20 Mar 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.90
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Biol. Unit 2: A (2x)
Keywords
:
Vizier; Viral Enzymes Involved In Replication; Dengue Virus Methyltransferase; Structural Genomics; Marseilles Structural Genomics Program @ Afmb; Msgp, Vizier. Viral Enzymes Involved In Replication, Viral Protein, Transferase
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Reference
:
M. P. Egloff, D. Benarroch, B. Selisko, J. L. Romette, B. Canard
An Rna Cap (Nucleoside-2'-O)-Methyltransferase In The Flavivirus Rna Polymerase Ns5: Crystal Structure And Functional Characterization
Embo J. V. 21 2757 2002
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Hetero Components
(3, 12)
Info
All Hetero Components
1a: GUANOSINE-5'-MONOPHOSPHATE (5GPa)
2a: S-ADENOSYL-L-HOMOCYSTEINE (SAHa)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
3f: SULFATE ION (SO4f)
3g: SULFATE ION (SO4g)
3h: SULFATE ION (SO4h)
3i: SULFATE ION (SO4i)
3j: SULFATE ION (SO4j)
View:
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Label:
No.
Name
Count
Type
Full Name
1
5GP
1
Ligand/Ion
GUANOSINE-5'-MONOPHOSPHATE
2
SAH
1
Ligand/Ion
S-ADENOSYL-L-HOMOCYSTEINE
3
SO4
10
Ligand/Ion
SULFATE ION
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Sites
(12, 12)
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)
View:
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:109 , HIS A:110 , GLU A:111 , SAH A:911
BINDING SITE FOR RESIDUE SO4 A 901
02
AC2
SOFTWARE
LYS A:105 , HIS A:110 , GLU A:149 , SER A:150 , SER A:151 , PRO A:152 , ARG A:160
BINDING SITE FOR RESIDUE SO4 A 902
03
AC3
SOFTWARE
ARG A:57 , LYS A:61
BINDING SITE FOR RESIDUE SO4 A 903
04
AC4
SOFTWARE
ARG A:38 , LYS A:42 , VAL A:55 , SER A:56 , ARG A:57 , ARG A:84
BINDING SITE FOR RESIDUE SO4 A 904
05
AC5
SOFTWARE
SER A:230 , ASN A:233 , ARG A:237
BINDING SITE FOR RESIDUE SO4 A 905
06
AC6
SOFTWARE
LYS A:12
BINDING SITE FOR RESIDUE SO4 A 906
07
AC7
SOFTWARE
LYS A:30 , ARG A:57 , ARG A:212
BINDING SITE FOR RESIDUE SO4 A 907
08
AC8
SOFTWARE
HIS A:52 , ARG A:246 , HIS A:247 , LYS A:248
BINDING SITE FOR RESIDUE SO4 A 908
09
AC9
SOFTWARE
LYS A:105 , ASP A:131 , ARG A:160 , ARG A:163 , SAH A:911
BINDING SITE FOR RESIDUE SO4 A 909
10
BC1
SOFTWARE
HIS A:52 , GLU A:67 , ARG A:68 , HIS A:247 , GLU A:253 , HOH A:920
BINDING SITE FOR RESIDUE SO4 A 910
11
BC2
SOFTWARE
SER A:56 , GLY A:58 , GLY A:81 , CYS A:82 , GLY A:83 , GLY A:86 , TRP A:87 , THR A:104 , LYS A:105 , VAL A:130 , ASP A:131 , VAL A:132 , PHE A:133 , ASP A:146 , SO4 A:901 , SO4 A:909 , HOH A:913
BINDING SITE FOR RESIDUE SAH A 911
12
BC3
SOFTWARE
LYS A:14 , LEU A:17 , ASN A:18 , LEU A:20 , PHE A:25 , LYS A:29 , SER A:150 , SER A:151 , PRO A:152
BINDING SITE FOR RESIDUE 5GP A 912
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(, 0)
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Exons
(0, 0)
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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
(1, 1)
Info
All SCOP Domains
1a: SCOP_d2p1da_ (A:)
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Protein Domains
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(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
S-adenosyl-L-methionine-dependent methyltransferases
(533)
Superfamily
:
S-adenosyl-L-methionine-dependent methyltransferases
(533)
Family
:
mRNA cap methylase
(41)
Protein domain
:
An RNA cap (nucleoside-2'-O-)-methyltransferase domain of RNA polymerase NS5
(14)
Flavivirus (Dengue virus type 2) [TaxId: 12637]
(8)
1a
d2p1da_
A:
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CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_2p1dA00 (A:7-265)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
Vaccinia Virus protein VP39
(378)
Dengue virus 2. Organism_taxid: 11060. Strain: type 2 new guinea.
(6)
1a
2p1dA00
A:7-265
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Pfam Domains
(2, 2)
Info
all PFAM domains
1a: PFAM_FtsJ_2p1dA01 (A:54-224)
2a: PFAM_Flavi_NS5_2p1dA02 (A:251-265)
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Clan
:
NADP_Rossmann
(1239)
Family
:
FtsJ
(23)
Dengue virus type 2 (strain Puerto Rico/PR159-S1/1969) (DENV-2)
(3)
1a
FtsJ-2p1dA01
A:54-224
Clan
:
RdRP
(210)
Family
:
Flavi_NS5
(21)
Dengue virus type 2 (strain Puerto Rico/PR159-S1/1969) (DENV-2)
(3)
2a
Flavi_NS5-2p1dA02
A:251-265
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Chain A
Asymmetric Unit 1
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Asym.Unit (50 KB)
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