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2X5O
Asym. Unit
Info
Asym.Unit (156 KB)
Biol.Unit 1 (151 KB)
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(1)
Title
:
DISCOVERY OF NOVEL 5-BENZYLIDENERHODANINE- AND 5-BENZYLIDENE-THIAZOLIDINE-2,4-DIONE INHIBITORS OF MURD LIGASE
Authors
:
N. Zidar, T. Tomasic, R. Sink, V. Rupnik, A. Kovac, S. Turk, C. Contreras A. Dessen, D. Blanot, S. Gobec, A. Zega, L. Peterlin-Masic, D. Kikelja
Date
:
10 Feb 10 (Deposition) - 15 Sep 10 (Release) - 31 Aug 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.46
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Atp-Binding, Cell Cycle, Cell Division, Cell Shape, Cell Wall Biogenesis/Degradation, Ligase, Peptidoglycan Synthesis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. Zidar, T. Tomasic, R. Sink, V. Rupnik, A. Kovac, S. Turk, D. Patin, D. Blanot, C. Contreras-Martel, A. Dessen, M. Muller-Premru, A. Zega S. Gobec, L. Peterlin-Masic, D. Kikelj
Discovery Of Novel 5-Benzylidenerhodanine And 5-Benzylidenethiazolidine-2, 4-Dione Inhibitors Of Murd Ligase.
J. Med. Chem. V. 53 6584 2010
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Hetero Components
(6, 10)
Info
All Hetero Components
1a: AZIDE ION (AZIa)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
3a: LYSINE NZ-CARBOXYLIC ACID (KCXa)
4a: SULFITE ION (SO3a)
5a: SULFATE ION (SO4a)
5b: SULFATE ION (SO4b)
6a: N-({3-[({4-[(Z)-(2,4-DIOXO-1,3-THI... (VSVa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AZI
1
Ligand/Ion
AZIDE ION
2
CL
4
Ligand/Ion
CHLORIDE ION
3
KCX
1
Mod. Amino Acid
LYSINE NZ-CARBOXYLIC ACID
4
SO3
1
Ligand/Ion
SULFITE ION
5
SO4
2
Ligand/Ion
SULFATE ION
6
VSV
1
Ligand/Ion
N-({3-[({4-[(Z)-(2,4-DIOXO-1,3-THIAZOLIDIN-5-YLIDENE)METHYL]PHENYL}AMINO)METHYL]PHENYL}CARBONYL)-D-GLUTAMICACID
[
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Sites
(8, 8)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:35 , THR A:36 , ARG A:37 , SER A:71 , PRO A:72 , GLY A:73 , PHE A:161 , HIS A:183 , LYS A:348 , ALA A:414 , SER A:415 , ASN A:421 , PHE A:422 , HOH A:2526 , HOH A:2527 , HOH A:2528 , HOH A:2529 , HOH A:2530 , HOH A:2531 , HOH A:2532
BINDING SITE FOR RESIDUE VSV A 500
2
AC2
SOFTWARE
ASP A:417 , GLN A:418 , PHE A:419 , LYS A:420
BINDING SITE FOR RESIDUE AZI A1443
3
AC3
SOFTWARE
ASN A:113 , GLY A:114 , LYS A:115 , SER A:116 , THR A:117 , ARG A:302 , HOH A:2533 , HOH A:2534
BINDING SITE FOR RESIDUE SO4 A1448
4
AC4
SOFTWARE
HIS A:309 , ASN A:310 , HIS A:439
BINDING SITE FOR RESIDUE SO4 A1450
5
AC5
SOFTWARE
GLY A:14 , LEU A:15 , THR A:16 , HOH A:2033 , HOH A:2075
BINDING SITE FOR RESIDUE SO3 A1451
6
AC6
SOFTWARE
ALA A:64 , HIS A:309 , ASN A:310 , HOH A:2069
BINDING SITE FOR RESIDUE CL A1453
7
AC7
SOFTWARE
LEU A:191 , GLN A:192 , GLU A:253 , LYS A:254
BINDING SITE FOR RESIDUE CL A1459
8
AC8
SOFTWARE
ASN A:363
BINDING SITE FOR RESIDUE CL A1505
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
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End label:
Sorry, no Info available
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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
(3, 3)
Info
All SCOP Domains
1a: SCOP_d2x5oa1 (A:1-93)
2a: SCOP_d2x5oa3 (A:298-439)
3a: SCOP_d2x5oa2 (A:94-297)
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Classes
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Folds
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Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
MurCD N-terminal domain
(22)
Superfamily
:
MurCD N-terminal domain
(22)
Family
:
automated matches
(11)
Protein domain
:
automated matches
(11)
Escherichia coli [TaxId: 668369]
(2)
1a
d2x5oa1
A:1-93
Fold
:
MurD-like peptide ligases, peptide-binding domain
(32)
Superfamily
:
MurD-like peptide ligases, peptide-binding domain
(32)
Family
:
automated matches
(11)
Protein domain
:
automated matches
(11)
Escherichia coli [TaxId: 668369]
(2)
2a
d2x5oa3
A:298-439
Fold
:
Ribokinase-like
(226)
Superfamily
:
MurD-like peptide ligases, catalytic domain
(32)
Family
:
MurCDEF
(23)
Protein domain
:
automated matches
(10)
Escherichia coli [TaxId: 668369]
(2)
3a
d2x5oa2
A:94-297
[
close SCOP info
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CATH Domains
(3, 3)
Info
all CATH domains
1a: CATH_2x5oA01 (A:1-92)
2a: CATH_2x5oA02 (A:93-298)
3a: CATH_2x5oA03 (A:299-433)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Escherichia coli. Organism_taxid: 668369. Strain: dh5[alpha].
(1)
1a
2x5oA01
A:1-92
Topology
:
UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
(109)
Homologous Superfamily
:
[code=3.40.1190.10, no name defined]
(36)
Escherichia coli. Organism_taxid: 668369. Strain: dh5[alpha].
(1)
2a
2x5oA02
A:93-298
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Protein-Tyrosine Phosphatase; Chain A
(262)
Homologous Superfamily
:
[code=3.90.190.20, no name defined]
(34)
Escherichia coli. Organism_taxid: 668369. Strain: dh5[alpha].
(1)
3a
2x5oA03
A:299-433
[
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Pfam Domains
(2, 2)
Info
all PFAM domains
1a: PFAM_Mur_ligase_C_2x5oA01 (A:299-378)
2a: PFAM_Mur_ligase_M_2x5oA02 (A:109-279)
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Clans
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)
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)
Families
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)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Mur_ligase_C]
(24)
Family
:
Mur_ligase_C
(24)
Escherichia coli (strain K12)
(14)
1a
Mur_ligase_C-2x5oA01
A:299-378
Clan
:
no clan defined [family: Mur_ligase_M]
(23)
Family
:
Mur_ligase_M
(23)
Escherichia coli (strain K12)
(14)
2a
Mur_ligase_M-2x5oA02
A:109-279
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Chain A
Asymmetric Unit 1
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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select non-helix/non-sheet protein parts
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Asym.Unit (156 KB)
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