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2VTD
Asym. Unit
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Asym.Unit (78 KB)
Biol.Unit 1 (74 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH D-GLU CONTAINING SULFONAMIDE INHIBITOR
Authors
:
J. Humljan, M. Kotnik, C. Contreras-Martel, D. Blanot, U. Urleb, A. Dessen, T. Solmajer, S. Gobec
Date
:
14 May 08 (Deposition) - 25 Nov 08 (Release) - 16 Mar 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.94
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Murd-Inhibitor Complex, Peptidoglycan Synthesis, Nucleotide-Binding, Sulfonamide Inhibitor, Murd Ligase, Atp-Binding, Cell Division, Ligase, Cytoplasm, Cell Shape, Cell Cycle, Cell Wall Biogenesis/Degradation
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
J. Humljan, M. Kotnik, C. Contreras-Martel, D. Blanot, U. Urleb, A. Dessen, T. Solmajer, S. Gobec
Novel Naphthalene-N-Sulfonyl-D-Glutamic Acid Derivatives As Inhibitors Of Murd, A Key Peptidoglycan Biosynthesis Enzyme.
J. Med. Chem. V. 51 7486 2008
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Hetero Components
(3, 3)
Info
All Hetero Components
1a: LYSINE NZ-CARBOXYLIC ACID (KCXa)
2a: N-({6-[(4-CYANO-2-FLUOROBENZYL)OXY... (LKMa)
3a: SULFATE ION (SO4a)
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No.
Name
Count
Type
Full Name
1
KCX
1
Mod. Amino Acid
LYSINE NZ-CARBOXYLIC ACID
2
LKM
1
Ligand/Ion
N-({6-[(4-CYANO-2-FLUOROBENZYL)OXY]NAPHTHALEN-2-YL}SULFONYL)-D-GLUTAMIC ACID
3
SO4
1
Ligand/Ion
SULFATE ION
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Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ILE A:11 , ASP A:35 , THR A:36 , ARG A:37 , PHE A:161 , HIS A:183 , LYS A:348 , ALA A:414 , SER A:415 , LEU A:416 , ASN A:421 , PHE A:422 , HOH A:2122 , HOH A:2136 , HOH A:2316
BINDING SITE FOR RESIDUE LKM A1441
2
AC2
SOFTWARE
ASN A:113 , GLY A:114 , LYS A:115 , SER A:116 , THR A:117 , ARG A:302 , LYS A:319 , HOH A:2205 , HOH A:2317
BINDING SITE FOR RESIDUE SO4 A1442
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
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Exons
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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_d2vtda1 (A:1-93)
2a: SCOP_d2vtda3 (A:298-440)
3a: SCOP_d2vtda2 (A:94-297)
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Protein Domains
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Organisms
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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: 562]
(8)
1a
d2vtda1
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: 562]
(8)
2a
d2vtda3
A:298-440
Fold
:
Ribokinase-like
(226)
Superfamily
:
MurD-like peptide ligases, catalytic domain
(32)
Family
:
MurCDEF
(23)
Protein domain
:
automated matches
(10)
Escherichia coli [TaxId: 562]
(8)
3a
d2vtda2
A:94-297
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CATH Domains
(3, 3)
Info
all CATH domains
1a: CATH_2vtdA01 (A:1-92)
2a: CATH_2vtdA02 (A:93-298)
3a: CATH_2vtdA03 (A:299-433)
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Organisms
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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.
(49)
1a
2vtdA01
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.
(11)
2a
2vtdA02
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.
(11)
3a
2vtdA03
A:299-433
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Pfam Domains
(2, 2)
Info
all PFAM domains
1a: PFAM_Mur_ligase_C_2vtdA01 (A:299-378)
2a: PFAM_Mur_ligase_M_2vtdA02 (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-2vtdA01
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-2vtdA02
A:109-279
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Chain A
Asymmetric Unit 1
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