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3IUB
Biol. Unit 1
Info
Asym.Unit (109 KB)
Biol.Unit 1 (103 KB)
Biol.Unit 2 (104 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF PANTOTHENATE SYNTHETASE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH 5-METHOXY-N-(5-METHYLPYRIDIN-2-YLSULFONYL)-1H-INDOLE-2-CARBOXAMIDE
Authors
:
H. L. Silvestre, A. W. Hung, S. Wen, A. Ciulli, T. L. Blundell, C. Abell
Date
:
31 Aug 09 (Deposition) - 13 Oct 09 (Release) - 10 Nov 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.50
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Biol. Unit 2: A,B (1x)
Keywords
:
Pantothenate Synthetase, Mycobacterium Tuberculosis, Fragment-Based Lead Discovery, Atp-Binding, Cytoplasm, Ligase, Magnesium, Metal-Binding, Nucleotide-Binding, Pantothenate Biosynthesis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. W. Hung, H. L. Silvestre, S. Wen, A. Ciulli, T. L. Blundell, C. Abell
Application Of Fragment Growing And Fragment Linking To The Discovery Of Inhibitors Of Mycobacterium Tuberculosis Pantothenate Synthetase.
Angew. Chem. Int. Ed. Engl. V. 48 8452 2009
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 17)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
1d: 1,2-ETHANEDIOL (EDOd)
1e: 1,2-ETHANEDIOL (EDOe)
1f: 1,2-ETHANEDIOL (EDOf)
1g: 1,2-ETHANEDIOL (EDOg)
1h: 1,2-ETHANEDIOL (EDOh)
1i: 1,2-ETHANEDIOL (EDOi)
1j: 1,2-ETHANEDIOL (EDOj)
1k: 1,2-ETHANEDIOL (EDOk)
1l: 1,2-ETHANEDIOL (EDOl)
2a: ETHANOL (EOHa)
2b: ETHANOL (EOHb)
3a: 5-METHOXY-N-[(5-METHYLPYRIDIN-2-YL... (FG2a)
3b: 5-METHOXY-N-[(5-METHYLPYRIDIN-2-YL... (FG2b)
3c: 5-METHOXY-N-[(5-METHYLPYRIDIN-2-YL... (FG2c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
12
Ligand/Ion
1,2-ETHANEDIOL
2
EOH
2
Ligand/Ion
ETHANOL
3
FG2
3
Ligand/Ion
5-METHOXY-N-[(5-METHYLPYRIDIN-2-YL)SULFONYL]-1H-INDOLE-2-CARBOXAMIDE
[
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]
Sites
(17, 17)
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)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HOH A:462 , HOH A:538 , HOH A:649 , EDO A:694
BINDING SITE FOR RESIDUE EOH A 689
02
AC2
SOFTWARE
ASN A:176 , HOH A:481 , HOH A:669 , ALA B:21
BINDING SITE FOR RESIDUE EOH A 691
03
AC3
SOFTWARE
MET A:71 , MET A:109 , TYR A:110 , GLY A:113 , ARG A:115 , THR A:116 , THR A:117 , LYS A:145 , ASP B:174
BINDING SITE FOR RESIDUE EDO A 692
04
AC4
SOFTWARE
GLU A:128 , ARG A:132 , HIS A:135 , HOH A:456 , HOH A:525 , HOH A:560
BINDING SITE FOR RESIDUE EDO A 693
05
AC5
SOFTWARE
PRO A:111 , ASP A:112 , HOH A:538 , EOH A:689
BINDING SITE FOR RESIDUE EDO A 694
06
AC6
SOFTWARE
PRO A:38 , MET A:40 , GLN A:72 , VAL A:142 , FG2 A:302 , HOH A:438 , HOH A:499
BINDING SITE FOR RESIDUE EDO A 696
07
AC7
SOFTWARE
THR A:218 , HOH A:361 , HIS B:222 , THR B:225
BINDING SITE FOR RESIDUE EDO A 698
08
AC8
SOFTWARE
PRO A:38 , THR A:39 , MET A:40 , HIS A:44 , GLY A:46 , HIS A:47 , TYR A:82 , LYS A:160 , ASP A:161 , GLN A:164 , PRO A:185 , THR A:186 , VAL A:187 , MET A:195 , HOH A:488 , HOH A:501 , HOH A:539 , HOH A:677 , HOH A:681 , EDO A:696
BINDING SITE FOR RESIDUE FG2 A 302
09
AC9
SOFTWARE
MET A:71 , LEU A:114 , PRO A:133 , THR A:134 , GLY A:138 , HOH A:457 , HOH A:505 , HOH A:526 , HOH A:545 , HOH A:615 , PHE B:6 , PRO B:8 , ALA B:26 , GLN B:119 , HOH B:523 , EDO B:699
BINDING SITE FOR RESIDUE FG2 A 303
10
BC1
SOFTWARE
ASP A:174 , MET B:109 , TYR B:110 , GLY B:113 , ARG B:115 , THR B:116 , LYS B:145 , HOH B:470
BINDING SITE FOR RESIDUE EDO B 690
11
BC2
SOFTWARE
GLN B:72 , VAL B:142 , FG2 B:302 , HOH B:310 , HOH B:524
BINDING SITE FOR RESIDUE EDO B 695
12
BC3
SOFTWARE
PRO B:243
BINDING SITE FOR RESIDUE EDO B 697
13
BC4
SOFTWARE
ARG A:115 , THR A:117 , FG2 A:303 , GLN B:119 , PRO B:120 , HOH B:377
BINDING SITE FOR RESIDUE EDO B 699
14
BC5
SOFTWARE
GLU B:128 , ARG B:132 , HIS B:135 , HOH B:457 , HOH B:562
BINDING SITE FOR RESIDUE EDO B 700
15
BC6
SOFTWARE
LEU B:123 , GLN B:170 , GLY B:256 , GLY B:258 , HOH B:306 , HOH B:414 , HOH B:478
BINDING SITE FOR RESIDUE EDO B 701
16
BC7
SOFTWARE
TYR B:162 , LEU B:165 , VAL B:166 , ARG B:169 , HOH B:336 , HOH B:438 , HOH B:624
BINDING SITE FOR RESIDUE EDO B 702
17
BC8
SOFTWARE
PRO B:38 , THR B:39 , MET B:40 , HIS B:44 , GLY B:46 , HIS B:47 , LYS B:160 , ASP B:161 , GLN B:164 , PRO B:185 , THR B:186 , VAL B:187 , MET B:195 , HOH B:497 , HOH B:511 , HOH B:535 , HOH B:602 , HOH B:680 , EDO B:695
BINDING SITE FOR RESIDUE FG2 B 302
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SAPs(SNPs)/Variants
(0, 0)
Info
(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, 2)
Info
All SCOP Domains
1a: SCOP_d3iuba_ (A:)
1b: SCOP_d3iubb_ (B:)
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Protein Domains
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(
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Organisms
(
)
(
)
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
d3iuba_
A:
1b
d3iubb_
B:
[
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_3iubB02 (B:186-288)
1b: CATH_3iubA02 (A:186-289)
2a: CATH_3iubA01 (A:4-185)
2b: CATH_3iubB01 (B:1-185)
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)
Organisms
(
)
(
)
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. Strain: h37rv.
(6)
1a
3iubB02
B:186-288
1b
3iubA02
A:186-289
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. Strain: h37rv.
(6)
2a
3iubA01
A:4-185
2b
3iubB01
B:1-185
[
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Pfam Domains
(0, 0)
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Asymmetric Unit 1
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Asym.Unit (109 KB)
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