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2WJP
Asym. Unit
Info
Asym.Unit (157 KB)
Biol.Unit 1 (151 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH D-GLU CONTAINING RHODANINE INHIBITOR
Authors
:
T. Tomasic, N. Zidar, R. Sink, A. Kovac, V. Rupnik, S. Turk, C. Contreras A. Dessen, D. Blanot, M. Muller-Premru, S. Gobec, A. Zega, L. Peterlin D. Kikelj
Date
:
28 May 09 (Deposition) - 25 Aug 10 (Release) - 26 Feb 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.60
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Peptidoglycan Synthesis, Cell Wall Biogenesis/Degradation, Cell Cycle, Cell Division, Ligase, Cell Shape 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
[
close entry info
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Hetero Components
(6, 19)
Info
All Hetero Components
1a: AZIDE ION (AZIa)
1b: AZIDE ION (AZIb)
1c: AZIDE ION (AZIc)
1d: AZIDE ION (AZId)
1e: AZIDE ION (AZIe)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
2e: CHLORIDE ION (CLe)
2f: CHLORIDE ION (CLf)
3a: N-({3-[({4-[(Z)-(4-OXO-2-THIOXO-1,... (D17a)
4a: DIMETHYL SULFOXIDE (DMSa)
5a: LYSINE NZ-CARBOXYLIC ACID (KCXa)
6a: SULFATE ION (SO4a)
6b: SULFATE ION (SO4b)
6c: SULFATE ION (SO4c)
6d: SULFATE ION (SO4d)
6e: SULFATE ION (SO4e)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AZI
5
Ligand/Ion
AZIDE ION
2
CL
6
Ligand/Ion
CHLORIDE ION
3
D17
1
Ligand/Ion
N-({3-[({4-[(Z)-(4-OXO-2-THIOXO-1,3-THIAZOLIDIN-5-YLIDENE)METHYL]PHENYL}AMINO)METHYL]PHENYL}CARBONYL)-L-GLUTAMIC ACID
4
DMS
1
Ligand/Ion
DIMETHYL SULFOXIDE
5
KCX
1
Mod. Amino Acid
LYSINE NZ-CARBOXYLIC ACID
6
SO4
5
Ligand/Ion
SULFATE ION
[
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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:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ILE A:11 , ASP A:35 , THR A:36 , ARG A:37 , SER A:71 , PRO A:72 , PHE A:161 , HIS A:183 , LYS A:348 , ALA A:414 , SER A:415 , LEU A:416 , ASN A:421 , PHE A:422 , SO4 A:1451 , HOH A:2525 , HOH A:2526 , HOH A:2528 , HOH A:2529 , HOH A:2530
BINDING SITE FOR RESIDUE D17 A1441
02
AC2
SOFTWARE
GLY A:73 , ARG A:186 , LEU A:416 , HOH A:2265 , HOH A:2529 , HOH A:2531
BINDING SITE FOR RESIDUE DMS A1442
03
AC3
SOFTWARE
ASP A:417 , GLN A:418 , PHE A:419
BINDING SITE FOR RESIDUE AZI A1443
04
AC4
SOFTWARE
ALA A:329 , ASN A:331 , LEU A:333 , HOH A:2532
BINDING SITE FOR RESIDUE AZI A1444
05
AC5
SOFTWARE
PRO A:300 , ARG A:302 , PHE A:422 , GLU A:423
BINDING SITE FOR RESIDUE AZI A1445
06
AC6
SOFTWARE
LEU A:339 , ASN A:363
BINDING SITE FOR RESIDUE AZI A1446
07
AC7
SOFTWARE
ALA A:102 , ALA A:104 , PRO A:105 , HOH A:2164
BINDING SITE FOR RESIDUE AZI A1447
08
AC8
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
09
AC9
SOFTWARE
THR A:166 , SER A:167 , SER A:168 , LEU A:169 , ARG A:200 , GLU A:203
BINDING SITE FOR RESIDUE SO4 A1449
10
BC1
SOFTWARE
HIS A:309 , ASN A:310 , SER A:438 , HIS A:439
BINDING SITE FOR RESIDUE SO4 A1450
11
BC2
SOFTWARE
GLY A:14 , LEU A:15 , THR A:16 , D17 A:1441 , HOH A:2024 , HOH A:2526 , HOH A:2535 , HOH A:2536
BINDING SITE FOR RESIDUE SO4 A1451
12
BC3
SOFTWARE
ARG A:37 , MET A:38 , GLN A:170 , HOH A:2537
BINDING SITE FOR RESIDUE SO4 A1452
13
BC4
SOFTWARE
HIS A:309 , ASN A:310 , HOH A:2055 , HOH A:2057
BINDING SITE FOR RESIDUE CL A1453
14
BC5
SOFTWARE
ARG A:395
BINDING SITE FOR RESIDUE CL A1454
15
BC6
SOFTWARE
TYR A:3 , GLN A:4 , ARG A:27
BINDING SITE FOR RESIDUE CL A1455
16
BC7
SOFTWARE
GLU A:96 , THR A:165 , SER A:167 , HOH A:2149
BINDING SITE FOR RESIDUE CL A1456
17
BC8
SOFTWARE
LEU A:57 , HOH A:2127
BINDING SITE FOR RESIDUE CL A1457
[
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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
;
View:
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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_d2wjpa1 (A:1-93)
2a: SCOP_d2wjpa3 (A:298-439)
3a: SCOP_d2wjpa2 (A:94-297)
View:
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Classes
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Folds
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Families
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)
(
)
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
d2wjpa1
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
d2wjpa3
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
d2wjpa2
A:94-297
[
close SCOP info
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CATH Domains
(3, 3)
Info
all CATH domains
1a: CATH_2wjpA01 (A:1-92)
2a: CATH_2wjpA02 (A:93-298)
3a: CATH_2wjpA03 (A:299-433)
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Classes
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)
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Architectures
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Topologies
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(
)
Homologous Superfamilies
(
)
(
)
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: 562. Cell_line: dh5a.
(1)
1a
2wjpA01
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: 562. Cell_line: dh5a.
(1)
2a
2wjpA02
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: 562. Cell_line: dh5a.
(1)
3a
2wjpA03
A:299-433
[
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]
Pfam Domains
(2, 2)
Info
all PFAM domains
1a: PFAM_Mur_ligase_C_2wjpA01 (A:299-378)
2a: PFAM_Mur_ligase_M_2wjpA02 (A:109-279)
View:
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Clans
(
)
(
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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-2wjpA01
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-2wjpA02
A:109-279
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]
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Protein & NOT PROSITE
Chain A
Asymmetric Unit 1
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