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2Y68
Asym. Unit
Info
Asym.Unit (161 KB)
Biol.Unit 1 (155 KB)
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(1)
Title
:
STRUCTURE-BASED DESIGN OF A NEW SERIES OF D-GLUTAMIC ACID-BASED INHIBITORS OF BACTERIAL MURD LIGASE
Authors
:
T. Tomasic, N. Zidar, R. Sink, A. Kovac, D. Patin, D. Blanot, C. Contrera A. Dessen, M. Muller-Premru, A. Zega, S. Gobec, L. Peterlin-Masic, D.
Date
:
20 Jan 11 (Deposition) - 08 Jun 11 (Release) - 31 Aug 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.49
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Atp-Binding, Cell Cycle, Cell Division, Cell Shape, Cell Wall, Cell Wall Biogenesis/Degradation, Ligase, Nucleotide-Binding, Peptidoglycan Synthesis, Uma
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
T. Tomasic, N. Zidar, R. Sink, A. Kovac, D. Blanot, C. Contreras-Martel, A. Dessen, M. Muller-Premru, A. Zega, S. Gobec, D. Kikelj, L. Peterlin Masic
Structure-Based Design Of A New Series Of D- Glutamic Acid-Based Inhibitors Of Bacterial Udp-N- Acetylmuramoyl-L-Alanine:D-Glutamate Ligase (Murd).
J. Med. Chem. V. 54 4600 2011
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Hetero Components
(6, 15)
Info
All Hetero Components
1a: AZIDE ION (AZIa)
1b: AZIDE ION (AZIb)
1c: AZIDE ION (AZIc)
1d: AZIDE ION (AZId)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
3a: DIMETHYL SULFOXIDE (DMSa)
3b: DIMETHYL SULFOXIDE (DMSb)
4a: LYSINE NZ-CARBOXYLIC ACID (KCXa)
5a: SULFATE ION (SO4a)
5b: SULFATE ION (SO4b)
5c: SULFATE ION (SO4c)
5d: SULFATE ION (SO4d)
6a: 2-[[2-FLUORO-5-[[[4-[(Z)-(4-OXO-2-... (T04a)
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No.
Name
Count
Type
Full Name
1
AZI
4
Ligand/Ion
AZIDE ION
2
CL
3
Ligand/Ion
CHLORIDE ION
3
DMS
2
Ligand/Ion
DIMETHYL SULFOXIDE
4
KCX
1
Mod. Amino Acid
LYSINE NZ-CARBOXYLIC ACID
5
SO4
4
Ligand/Ion
SULFATE ION
6
T04
1
Ligand/Ion
2-[[2-FLUORO-5-[[[4-[(Z)-(4-OXO-2-SULFANYLIDENE-1,3-THIAZOLIDIN-5-YLIDENE)METHYL]PHENYL]AMINO]METHYL]PHENYL]CARBONYLAMINO]PENTANEDIOIC ACID
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Sites
(13, 13)
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)
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ILE A:11 , ASP A:35 , THR A:36 , ARG A:37 , SER A:71 , ASN A:138 , PHE A:161 , HIS A:183 , LYS A:348 , ALA A:414 , SER A:415 , ASN A:421 , PHE A:422 , SO4 A:1442 , HOH A:2166 , HOH A:2193 , HOH A:2234 , HOH A:2439 , HOH A:2440 , HOH A:2441 , HOH A:2443 , HOH A:2447
BINDING SITE FOR RESIDUE T04 A 500
02
AC2
SOFTWARE
LEU A:163 , THR A:166 , SER A:167 , SER A:168 , LEU A:169 , ARG A:200 , GLU A:203
BINDING SITE FOR RESIDUE DMS A 601
03
AC3
SOFTWARE
ASN A:7 , ARG A:32 , ALA A:64 , GLU A:308 , HIS A:309 , ASN A:310
BINDING SITE FOR RESIDUE DMS A 604
04
AC4
SOFTWARE
GLN A:418 , PHE A:419
BINDING SITE FOR RESIDUE AZI A 700
05
AC5
SOFTWARE
ALA A:329 , ASN A:331 , GLY A:332 , LEU A:333
BINDING SITE FOR RESIDUE AZI A 701
06
AC6
SOFTWARE
LEU A:339 , ASN A:363 , VAL A:364
BINDING SITE FOR RESIDUE AZI A 703
07
AC7
SOFTWARE
ALA A:104 , PRO A:105 , HOH A:2138 , HOH A:2444
BINDING SITE FOR RESIDUE AZI A 704
08
AC8
SOFTWARE
ASN A:113 , GLY A:114 , LYS A:115 , SER A:116 , THR A:117 , ARG A:302 , HOH A:2445 , HOH A:2446
BINDING SITE FOR RESIDUE SO4 A1440
09
AC9
SOFTWARE
HIS A:309 , ASN A:310 , SER A:438 , HIS A:439
BINDING SITE FOR RESIDUE SO4 A1441
10
BC1
SOFTWARE
GLY A:14 , LEU A:15 , THR A:16 , T04 A:500 , HOH A:2447 , HOH A:2448 , HOH A:2449
BINDING SITE FOR RESIDUE SO4 A1442
11
BC2
SOFTWARE
ARG A:37 , MET A:38 , GLN A:170
BINDING SITE FOR RESIDUE SO4 A1443
12
BC3
SOFTWARE
ARG A:395
BINDING SITE FOR RESIDUE CL A1444
13
BC4
SOFTWARE
SER A:56 , LEU A:57 , HOH A:2103
BINDING SITE FOR RESIDUE CL A1445
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
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Exons
(0, 0)
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(0, 0)
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CATH Domains
(0, 0)
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all CATH domains
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Pfam Domains
(2, 2)
Info
all PFAM domains
1a: PFAM_Mur_ligase_C_2y68A01 (A:299-378)
2a: PFAM_Mur_ligase_M_2y68A02 (A:109-279)
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Clans
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Clan
:
no clan defined [family: Mur_ligase_C]
(24)
Family
:
Mur_ligase_C
(24)
Escherichia coli (strain K12)
(14)
1a
Mur_ligase_C-2y68A01
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-2y68A02
A:109-279
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Chain A
Asymmetric Unit 1
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