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1SJN
Asym. Unit
Info
Asym.Unit (77 KB)
Biol.Unit 1 (69 KB)
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(1)
Title
:
MYCOBACTERIUM TUBERCULOSIS DUTPASE COMPLEXED WITH MAGNESIUM AND ALPHA, BETA-IMIDO-DUTP
Authors
:
M. R. Sawaya, S. Chan, B. Segelke, T. Lekin, H. Krupka, U. S. Cho, M. -Y. Ki C. -Y. Kim, C. M. Naranjo, Y. C. Rogers, M. S. Park, G. S. Waldo, I. Pashko D. Cascio, T. O. Yeates, J. L. Perry, T. C. Terwilliger, D. Eisenberg, T Structural Genomics Consortium (Tbsgc)
Date
:
04 Mar 04 (Deposition) - 09 Mar 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Jelly-Roll, Structural Genomics, Psi, Protein Structure Initiative, Tb Structural Genomics Consortium, Tbsgc, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Chan, B. Segelke, T. Lekin, H. Krupka, U. S. Cho, M. -Y. Kim, M. So, C. -Y. Kim, C. M. Naranjo, Y. C. Rogers, M. S. Park, G. S. Waldo, I. Pashkov, D. Cascio, J. L. Perry, M. R. Sawaya
Crystal Structure Of The Mycobacterium Tuberculosis Dutpase Insights Into The Catalytic Mechanism.
J. Mol. Biol. V. 341 503 2004
[
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Hetero Components
(4, 9)
Info
All Hetero Components
1a: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMID... (DUPa)
1b: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMID... (DUPb)
1c: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMID... (DUPc)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
3a: NITRATE ION (NO3a)
3b: NITRATE ION (NO3b)
4a: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DUP
3
Ligand/Ion
2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
2
MG
3
Ligand/Ion
MAGNESIUM ION
3
NO3
2
Ligand/Ion
NITRATE ION
4
TRS
1
Ligand/Ion
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
[
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Sites
(9, 9)
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)
9: AC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HOH A:1218 , HOH A:1221 , DUP B:3170 , HOH B:3212
BINDING SITE FOR RESIDUE MG A 171
2
AC2
SOFTWARE
DUP A:1170 , HOH A:1220 , HOH C:192 , HOH C:217
BINDING SITE FOR RESIDUE MG C 171
3
AC3
SOFTWARE
DUP B:2170 , HOH B:3174 , HOH B:3207 , HOH B:3239
BINDING SITE FOR RESIDUE MG B 171
4
AC4
SOFTWARE
PHE A:130 , ASP A:131 , THR B:4 , ALA B:6 , ARG C:87 , VAL C:127
BINDING SITE FOR RESIDUE NO3 C 172
5
AC5
SOFTWARE
GLY B:66 , LEU B:67 , ARG B:70 , VAL B:127 , ALA B:133 , HOH B:3210 , HOH B:3220
BINDING SITE FOR RESIDUE NO3 B 172
6
AC6
SOFTWARE
ASN A:77 , GLY A:80 , THR A:81 , ILE A:82 , ASP A:83 , TYR A:86 , ILE A:90 , LYS A:91 , HOH A:1172 , HOH A:1177 , HOH A:1178 , HOH A:1186 , HOH A:1202 , HOH A:1210 , HOH A:1220 , HOH A:1226 , HOH A:1231 , ARG B:140 , ARG C:64 , SER C:65 , GLY C:66 , GLN C:113 , MG C:171 , HOH C:192 , HOH C:202 , HOH C:217
BINDING SITE FOR RESIDUE DUP A 1170
7
AC7
SOFTWARE
PRO B:63 , ARG B:64 , SER B:65 , GLY B:66 , GLN B:113 , MG B:171 , HOH B:3174 , HOH B:3178 , HOH B:3207 , HOH B:3210 , HOH B:3220 , HOH B:3222 , HOH B:3226 , HOH B:3229 , HOH B:3231 , HOH B:3236 , HOH B:3238 , HOH B:3239 , ASN C:77 , GLY C:80 , THR C:81 , ILE C:82 , ASP C:83 , TYR C:86 , ILE C:90 , LYS C:91 , HOH C:175
BINDING SITE FOR RESIDUE DUP B 2170
8
AC8
SOFTWARE
ARG A:64 , SER A:65 , GLY A:66 , MG A:171 , HOH A:1218 , HOH A:1221 , ASN B:77 , GLY B:80 , THR B:81 , ILE B:82 , ASP B:83 , TYR B:86 , ILE B:90 , LYS B:91 , HOH B:3172 , HOH B:3186 , HOH B:3188 , HOH B:3212 , HOH B:3214 , HOH B:3233 , HOH B:3242 , ARG C:140 , GLY C:144 , HIS C:145
BINDING SITE FOR RESIDUE DUP B 3170
9
AC9
SOFTWARE
SER A:74 , ILE A:75 , VAL A:76 , HOH A:1174 , SER B:74 , ILE B:75 , VAL B:76 , HOH B:3179 , SER C:74 , ILE C:75 , VAL C:76 , HOH C:215
BINDING SITE FOR RESIDUE TRS A 1171
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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Sorry, no Info available
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Exons
(0, 0)
Info
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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
(1, 3)
Info
All SCOP Domains
1a: SCOP_d1sjna_ (A:)
1b: SCOP_d1sjnb_ (B:)
1c: SCOP_d1sjnc_ (C:)
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
beta-clip
(280)
Superfamily
:
dUTPase-like
(122)
Family
:
dUTPase-like
(71)
Protein domain
:
Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase)
(36)
Mycobacterium tuberculosis, rv2697c [TaxId: 1773]
(8)
1a
d1sjna_
A:
1b
d1sjnb_
B:
1c
d1sjnc_
C:
[
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CATH Domains
(1, 3)
Info
all CATH domains
1a: CATH_1sjnB00 (B:1-140)
1b: CATH_1sjnC00 (C:2-145)
1c: CATH_1sjnA00 (A:2-132)
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)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Distorted Sandwich
(506)
Topology
:
Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A
(52)
Homologous Superfamily
:
[code=2.70.40.10, no name defined]
(51)
Mycobacterium tuberculosis. Organism_taxid: 1773.
(8)
1a
1sjnB00
B:1-140
1b
1sjnC00
C:2-145
1c
1sjnA00
A:2-132
[
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Pfam Domains
(1, 3)
Info
all PFAM domains
1a: PFAM_dUTPase_1sjnC01 (C:14-145)
1b: PFAM_dUTPase_1sjnC02 (C:14-145)
1c: PFAM_dUTPase_1sjnC03 (C:14-145)
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Clans
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)
Organisms
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)
Clan
:
dUTPase
(38)
Family
:
dUTPase
(38)
Mycobacterium tuberculosis
(9)
1a
dUTPase-1sjnC01
C:14-145
1b
dUTPase-1sjnC02
C:14-145
1c
dUTPase-1sjnC03
C:14-145
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Asymmetric Unit 1
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select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
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select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
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show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
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