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1E4E
Biol. Unit 1
Info
Asym.Unit (127 KB)
Biol.Unit 1 (232 KB)
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(1)
Title
:
D-ALANYL-D-LACATE LIGASE
Authors
:
D. I. Roper
Date
:
03 Jul 00 (Deposition) - 28 Jun 01 (Release) - 21 Sep 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (2x)
Keywords
:
Ligase, Cell Wall, Antibiotic Resistance, Membrane, Peptidoglycan Synthesis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. I. Roper, T. Huyton, A. Vagin, G. Dodson
The Molecular Basis Of Vancomycin Resistance In Clinically Releveant Enterococci: Crsytal Structure Of D-Alanyl-D-Lactate Ligase (Vana)
Proc. Natl. Acad. Sci. Usa V. 97 8921 2000
[
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Hetero Components
(4, 42)
Info
All Hetero Components
1a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
1b: ADENOSINE-5'-DIPHOSPHATE (ADPb)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
2h: GLYCEROL (GOLh)
2i: GLYCEROL (GOLi)
2j: GLYCEROL (GOLj)
2k: GLYCEROL (GOLk)
2l: GLYCEROL (GOLl)
2m: GLYCEROL (GOLm)
2n: GLYCEROL (GOLn)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
4a: 1(S)-AMINOETHYL-(2-CARBOXYPROPYL)P... (PHYa)
4b: 1(S)-AMINOETHYL-(2-CARBOXYPROPYL)P... (PHYb)
5a: SULFATE ION (SO4a)
5b: SULFATE ION (SO4b)
5c: SULFATE ION (SO4c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ADP
4
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
GOL
28
Ligand/Ion
GLYCEROL
3
MG
-1
Ligand/Ion
MAGNESIUM ION
4
PHY
4
Ligand/Ion
1(S)-AMINOETHYL-(2-CARBOXYPROPYL)PHOSPHORYL-PHOSPHINIC ACID
5
SO4
6
Ligand/Ion
SULFATE ION
[
close Hetero Component info
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Sites
(25, 25)
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)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LYS A:133 , PHE A:169 , LYS A:171 , SER A:175 , GLY A:176 , SER A:177 , SER A:178 , GLU A:207 , GLN A:208 , VAL A:210 , GLU A:214 , LEU A:236 , ILE A:240 , PHE A:241 , PHE A:294 , ASN A:304 , GLU A:305 , PHY A:355 , MG A:360 , MG A:365 , HOH A:2095 , HOH A:2112 , HOH A:2151 , HOH A:2166 , HOH A:2167
BINDING SITE FOR RESIDUE ADP A 350
02
AC2
SOFTWARE
GLU A:16 , SER A:177 , PHE A:241 , ILE A:243 , HIS A:244 , ARG A:290 , GLU A:305 , ASN A:307 , GLY A:311 , SER A:316 , ARG A:317 , ADP A:350 , MG A:360 , MG A:365 , HOH A:2097 , HOH A:2154 , HOH A:2167 , HOH A:2168 , HOH A:2169
BINDING SITE FOR RESIDUE PHY A 355
03
AC3
SOFTWARE
GLU A:305 , ASN A:307 , ADP A:350 , PHY A:355 , HOH A:2095
BINDING SITE FOR RESIDUE MG A 360
04
AC4
SOFTWARE
GLU A:305 , ADP A:350 , PHY A:355 , HOH A:2151 , HOH A:2167
BINDING SITE FOR RESIDUE MG A 365
05
AC5
SOFTWARE
LYS B:133 , PHE B:169 , LYS B:171 , GLY B:176 , SER B:177 , SER B:178 , GLU B:207 , GLN B:208 , ALA B:209 , VAL B:210 , GLU B:214 , LEU B:236 , ILE B:240 , PHE B:241 , PHE B:294 , ASN B:304 , GLU B:305 , PHY B:355 , MG B:360 , MG B:365 , HOH B:2150 , HOH B:2171 , HOH B:2172
BINDING SITE FOR RESIDUE ADP B 350
06
AC6
SOFTWARE
GLU B:16 , SER B:177 , HIS B:244 , ARG B:290 , GLU B:305 , ASN B:307 , GLY B:311 , SER B:316 , ARG B:317 , ADP B:350 , MG B:360 , MG B:365 , HOH B:2054 , HOH B:2096 , HOH B:2160 , HOH B:2171 , HOH B:2173
BINDING SITE FOR RESIDUE PHY B 355
07
AC7
SOFTWARE
GLY B:176 , GLU B:305 , ASN B:307 , ADP B:350 , PHY B:355 , HOH B:2094
BINDING SITE FOR RESIDUE MG B 360
08
AC8
SOFTWARE
GLU B:305 , ADP B:350 , PHY B:355 , HOH B:2150 , HOH B:2171
BINDING SITE FOR RESIDUE MG B 365
09
AC9
SOFTWARE
HOH A:2143 , ARG B:174 , LYS B:203 , HOH B:2103 , HOH B:3002
BINDING SITE FOR RESIDUE SO4 B1342
10
BC1
SOFTWARE
ARG A:174 , LYS A:203 , HOH A:2109 , HOH A:3003 , HOH A:3004 , HOH B:2068
BINDING SITE FOR RESIDUE SO4 A1343
11
BC2
SOFTWARE
ASP A:105 , ARG A:174 , HOH A:3007 , HOH A:3008 , GLN B:125 , HOH B:3009 , HOH B:3010
BINDING SITE FOR RESIDUE SO4 A1344
12
BC3
SOFTWARE
SER A:66 , LYS A:81 , ARG A:242 , GLN A:245 , GLU A:246 , VAL A:247
BINDING SITE FOR RESIDUE GOL A1345
13
BC4
SOFTWARE
SER B:265 , ALA B:266
BINDING SITE FOR RESIDUE GOL B1343
14
BC5
SOFTWARE
ARG B:3 , LYS B:33 , GLU B:34
BINDING SITE FOR RESIDUE GOL B1344
15
BC6
SOFTWARE
LEU B:339 , ALA B:340 , LEU B:341
BINDING SITE FOR RESIDUE GOL B1345
16
BC7
SOFTWARE
GLU A:62 , LYS A:183 , TYR A:238 , GLY A:239
BINDING SITE FOR RESIDUE GOL A1346
17
BC8
SOFTWARE
HIS A:84 , SER A:178 , ARG A:242 , GLN A:245
BINDING SITE FOR RESIDUE GOL A1347
18
BC9
SOFTWARE
ASN A:2 , ARG A:3
BINDING SITE FOR RESIDUE GOL A1348
19
CC1
SOFTWARE
LYS A:155 , GLU A:195 , HOH A:2106
BINDING SITE FOR RESIDUE GOL A1349
20
CC2
SOFTWARE
GLU B:37 , LEU B:39 , MET B:51 , ASN B:89
BINDING SITE FOR RESIDUE GOL B1346
21
CC3
SOFTWARE
GLU B:26 , PHE B:312 , THR B:313 , SER B:314 , LEU B:329 , HOH B:3011
BINDING SITE FOR RESIDUE GOL B1347
22
CC4
SOFTWARE
GLU A:62 , ASN A:63 , CYS A:64 , TYR A:65 , SER A:66
BINDING SITE FOR RESIDUE GOL A 990
23
CC5
SOFTWARE
LYS A:155
BINDING SITE FOR RESIDUE GOL A 996
24
CC6
SOFTWARE
LYS A:5 , GLU A:37 , ASN A:89
BINDING SITE FOR RESIDUE GOL A1350
25
CC7
SOFTWARE
LYS B:50 , TYR B:65 , HOH B:3012 , HOH B:3013
BINDING SITE FOR RESIDUE GOL B1348
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: DALA_DALA_LIGASE_1 (A:99-110,B:99-110)
2: DALA_DALA_LIGASE_2 (A:283-311,B:283-311)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DALA_DALA_LIGASE_1
PS00843
D-alanine--D-alanine ligase signature 1.
VANA_ENTFC
99-110
4
A:99-110
B:99-110
2
DALA_DALA_LIGASE_2
PS00844
D-alanine--D-alanine ligase signature 2.
VANA_ENTFC
283-311
4
A:283-311
B:283-311
[
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1e4ea2 (A:132-342)
1b: SCOP_d1e4eb2 (B:132-341)
2a: SCOP_d1e4ea1 (A:2-131)
2b: SCOP_d1e4eb1 (B:2-131)
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
ATP-grasp
(191)
Superfamily
:
Glutathione synthetase ATP-binding domain-like
(158)
Family
:
ATP-binding domain of peptide synthetases
(9)
Protein domain
:
D-alanine:D-lactate ligase VanA, C-domain
(2)
Enterococcus faecium [TaxId: 1352]
(1)
1a
d1e4ea2
A:132-342
1b
d1e4eb2
B:132-341
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
PreATP-grasp domain
(131)
Superfamily
:
PreATP-grasp domain
(131)
Family
:
D-Alanine ligase N-terminal domain
(7)
Protein domain
:
D-alanine:D-lactate ligase VanA, N-domain
(2)
Enterococcus faecium [TaxId: 1352]
(1)
2a
d1e4ea1
A:2-131
2b
d1e4eb1
B:2-131
[
close SCOP info
]
CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_1e4eA01 (A:122-146,A:211-342)
1b: CATH_1e4eB01 (B:122-146,B:211-341)
2a: CATH_1e4eA02 (A:149-206)
2b: CATH_1e4eB02 (B:149-206)
3a: CATH_1e4eA03 (A:2-121)
3b: CATH_1e4eB03 (B:2-121)
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Architectures
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Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
D-amino Acid Aminotransferase; Chain A, domain 1
(175)
Homologous Superfamily
:
ATP-grasp fold, B domain
(118)
Enterococcus faecium. Organism_taxid: 1352. Strain: bm41417.
(1)
1a
1e4eA01
A:122-146,A:211-342
1b
1e4eB01
B:122-146,B:211-341
Topology
:
Dna Ligase; domain 1
(375)
Homologous Superfamily
:
ATP-grasp fold, A domain
(109)
Enterococcus faecium. Organism_taxid: 1352. Strain: bm41417.
(1)
2a
1e4eA02
A:149-206
2b
1e4eB02
B:149-206
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.20, no name defined]
(85)
Enterococcus faecium. Organism_taxid: 1352. Strain: bm41417.
(1)
3a
1e4eA03
A:2-121
3b
1e4eB03
B:2-121
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Atom Selection
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select chains 'A' and 'C'
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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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show SS bonds with a radius of 100 units (=0.4Å)
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