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3IOD
Asym. Unit
Info
Asym.Unit (99 KB)
Biol.Unit 1 (94 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS PANTOTHENATE SYNTHETASE AT 1.75 ANG RESOLUTION IN COMPLEX WITH 5'-DEOXY-5'-((3-NITROBENZYL)DISULFANYL)-ADENOSINE
Authors
:
A. Ciulli, D. E. Scott, C. Abell
Date
:
14 Aug 09 (Deposition) - 01 Dec 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.75
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Mycobacterium Tuberculosis, Pantothenate Biosynthesis, Enzymes, Ligase, Inhibitors, Drug Design, Fragment-Based, Dynamic Combinatorial Chemistry, Atp-Binding, Magnesium, Metal-Binding, Nucleotide-Binding
(Keyword Search:
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Reference
:
D. E. Scott, G. J. Dawes, M. Ando, C. Abell, A. Ciulli
A Fragment-Based Approach To Probing Adenosine Recognition Sites By Using Dynamic Combinatorial Chemistry
Chembiochem V. 10 2772 2009
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Hetero Components
(4, 9)
Info
All Hetero Components
1a: (2R,3R,4S,5S)-2-(6-AMINO-9H-PURIN-... (A6Da)
1b: (2R,3R,4S,5S)-2-(6-AMINO-9H-PURIN-... (A6Db)
2a: ETHANOL (EOHa)
2b: ETHANOL (EOHb)
2c: ETHANOL (EOHc)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
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No.
Name
Count
Type
Full Name
1
A6D
2
Ligand/Ion
(2R,3R,4S,5S)-2-(6-AMINO-9H-PURIN-9-YL)-5-{[(3-NITROBENZYL)DISULFANYL]METHYL}TETRAHYDROFURAN-3,4-DIOL
2
EOH
3
Ligand/Ion
ETHANOL
3
GOL
2
Ligand/Ion
GLYCEROL
4
SO4
2
Ligand/Ion
SULFATE ION
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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)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
PRO A:38 , THR A:39 , MET A:40 , HIS A:44 , GLY A:46 , HIS A:47 , PHE A:67 , GLN A:72 , VAL A:142 , LEU A:146 , PHE A:157 , GLY A:158 , LYS A:160 , ASP A:161 , GLN A:164 , THR A:186 , VAL A:187 , MET A:195 , HOH A:301 , HOH A:314 , SO4 A:703
BINDING SITE FOR RESIDUE A6D A 302
2
AC2
SOFTWARE
HIS A:44 , HIS A:47 , LYS A:160 , SER A:196 , SER A:197 , ARG A:198 , A6D A:302
BINDING SITE FOR RESIDUE SO4 A 703
3
AC3
SOFTWARE
MET A:109 , TYR A:110 , PRO A:111 , ASP A:112 , GLY A:113 , ARG A:115 , THR A:116 , LYS A:145 , ASP B:174
BINDING SITE FOR RESIDUE GOL A 701
4
AC4
SOFTWARE
PRO A:111 , ASP A:112 , HOH A:340
BINDING SITE FOR RESIDUE GOL A 708
5
AC5
SOFTWARE
LEU A:114 , ARG A:115 , THR A:117 , HOH A:640 , GLN B:119 , PRO B:120
BINDING SITE FOR RESIDUE EOH A 710
6
AC6
SOFTWARE
THR A:218 , HIS B:222 , THR B:225
BINDING SITE FOR RESIDUE EOH A 711
7
AC7
SOFTWARE
PRO B:38 , THR B:39 , MET B:40 , HIS B:44 , GLY B:46 , HIS B:47 , LEU B:50 , PHE B:67 , ASN B:69 , VAL B:142 , LEU B:146 , PHE B:157 , GLY B:158 , LYS B:160 , ASP B:161 , GLN B:164 , THR B:186 , VAL B:187 , MET B:195 , HOH B:312 , HOH B:324 , SO4 B:704
BINDING SITE FOR RESIDUE A6D B 301
8
AC8
SOFTWARE
HIS B:44 , HIS B:47 , LYS B:160 , SER B:196 , SER B:197 , A6D B:301 , HOH B:344 , HOH B:388 , HOH B:687
BINDING SITE FOR RESIDUE SO4 B 704
9
AC9
SOFTWARE
ARG A:169 , ALA A:173 , ARG B:115 , HOH B:525
BINDING SITE FOR RESIDUE EOH B 712
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 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.
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d3ioda_ (A:)
1b: SCOP_d3iodb_ (B:)
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Protein Domains
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(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Adenine nucleotide alpha hydrolase-like
(440)
Superfamily
:
Nucleotidylyl transferase
(325)
Family
:
Pantothenate synthetase (Pantoate-beta-alanine ligase, PanC)
(46)
Protein domain
:
Pantothenate synthetase (Pantoate-beta-alanine ligase, PanC)
(44)
Mycobacterium tuberculosis [TaxId: 1773]
(39)
1a
d3ioda_
A:
1b
d3iodb_
B:
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_3iodB02 (B:186-288)
1b: CATH_3iodA02 (A:186-288)
2a: CATH_3iodA01 (A:4-185)
2b: CATH_3iodB01 (B:2-185)
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Organisms
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Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Pantoate--beta-alanine Ligase; Chain: A,domain 2
(43)
Homologous Superfamily
:
[code=3.30.1300.10, no name defined]
(36)
Mycobacterium tuberculosis. Organism_taxid: 1773.
(19)
1a
3iodB02
B:186-288
1b
3iodA02
A:186-288
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1
(328)
Mycobacterium tuberculosis. Organism_taxid: 1773.
(20)
2a
3iodA01
A:4-185
2b
3iodB01
B:2-185
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Pfam Domains
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Asymmetric Unit 1
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