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2WKE
Asym. Unit
Info
Asym.Unit (295 KB)
Biol.Unit 1 (76 KB)
Biol.Unit 2 (75 KB)
Biol.Unit 3 (75 KB)
Biol.Unit 4 (75 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE ACTINOMADURA R39 DD-PEPTIDASE INHIBITED BY 6-BETA-IODOPENICILLANATE.
Authors
:
E. Sauvage, R. Herman, F. Kerff, P. Charlier
Date
:
10 Jun 09 (Deposition) - 01 Dec 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Hydrolase, Antibiotic Resistance, Actinomadura, Penicillin Binding, Iodopenicillanate
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Sauvage, A. Zervosen, G. Dive, R. Herman, A. Amoroso, B. Joris, E. Fonze, R. F. Pratt, A. Luxen, P. Charlier, F. Kerff
Structural Basis Of The Inhibition Of Class A Beta- Lactamases And Penicillin-Binding Proteins By 6- Beta-Iodopenicillanate.
J. Am. Chem. Soc. V. 131 15262 2009
[
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Hetero Components
(3, 38)
Info
All Hetero Components
1a: (3S)-2,2-DIMETHYL-3,4-DIHYDRO-2H-1... (BIYa)
1b: (3S)-2,2-DIMETHYL-3,4-DIHYDRO-2H-1... (BIYb)
1c: (3S)-2,2-DIMETHYL-3,4-DIHYDRO-2H-1... (BIYc)
1d: (3S)-2,2-DIMETHYL-3,4-DIHYDRO-2H-1... (BIYd)
2a: COBALT (II) ION (COa)
2b: COBALT (II) ION (COb)
2c: COBALT (II) ION (COc)
2d: COBALT (II) ION (COd)
2e: COBALT (II) ION (COe)
2f: COBALT (II) ION (COf)
2g: COBALT (II) ION (COg)
2h: COBALT (II) ION (COh)
2i: COBALT (II) ION (COi)
2j: COBALT (II) ION (COj)
2k: COBALT (II) ION (COk)
2l: COBALT (II) ION (COl)
2m: COBALT (II) ION (COm)
2n: COBALT (II) ION (COn)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
3f: SULFATE ION (SO4f)
3g: SULFATE ION (SO4g)
3h: SULFATE ION (SO4h)
3i: SULFATE ION (SO4i)
3j: SULFATE ION (SO4j)
3k: SULFATE ION (SO4k)
3l: SULFATE ION (SO4l)
3m: SULFATE ION (SO4m)
3n: SULFATE ION (SO4n)
3o: SULFATE ION (SO4o)
3p: SULFATE ION (SO4p)
3q: SULFATE ION (SO4q)
3r: SULFATE ION (SO4r)
3s: SULFATE ION (SO4s)
3t: SULFATE ION (SO4t)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BIY
4
Ligand/Ion
(3S)-2,2-DIMETHYL-3,4-DIHYDRO-2H-1,4-THIAZINE-3,6-DICARBOXYLIC ACID
2
CO
14
Ligand/Ion
COBALT (II) ION
3
SO4
20
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(38, 38)
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)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ALA A:48 , SER A:49 , TYR A:147 , SER A:298 , ASN A:300 , GLY A:412 , THR A:413 , ALA B:175
BINDING SITE FOR RESIDUE BIY A 500
02
AC2
SOFTWARE
HIS A:282 , THR A:283 , HOH A:2044
BINDING SITE FOR RESIDUE SO4 A 601
03
AC3
SOFTWARE
ALA A:234 , ARG A:236 , HOH A:2167
BINDING SITE FOR RESIDUE SO4 A 602
04
AC4
SOFTWARE
ASP A:211 , PRO A:213 , VAL A:214 , HOH A:2168
BINDING SITE FOR RESIDUE SO4 A 603
05
AC5
SOFTWARE
SER A:131 , GLU A:132 , ARG A:133 , LEU A:134
BINDING SITE FOR RESIDUE SO4 A 604
06
AC6
SOFTWARE
THR A:97 , ASP A:102 , HIS A:282 , HOH A:2035
BINDING SITE FOR RESIDUE SO4 A 605
07
AC7
SOFTWARE
GLU A:188 , HIS A:247 , GLU A:251 , HOH A:2169
BINDING SITE FOR RESIDUE CO A 610
08
AC8
SOFTWARE
HIS A:462 , HOH A:2170
BINDING SITE FOR RESIDUE CO A 611
09
AC9
SOFTWARE
LEU A:63 , HIS A:67
BINDING SITE FOR RESIDUE CO A 612
10
BC1
SOFTWARE
HIS A:158 , GLU A:168
BINDING SITE FOR RESIDUE CO A 613
11
BC2
SOFTWARE
ALA B:48 , SER B:49 , TYR B:147 , SER B:298 , ASN B:300 , GLY B:412 , THR B:413 , HOH B:2129 , HOH B:2141
BINDING SITE FOR RESIDUE BIY B 500
12
BC3
SOFTWARE
HIS B:282 , THR B:283 , HOH B:2098
BINDING SITE FOR RESIDUE SO4 B 601
13
BC4
SOFTWARE
ALA B:234 , ARG B:236
BINDING SITE FOR RESIDUE SO4 B 602
14
BC5
SOFTWARE
TRP B:139 , SER B:415 , HOH B:2142
BINDING SITE FOR RESIDUE SO4 B 603
15
BC6
SOFTWARE
SER B:131 , ARG B:133 , LEU B:134 , HOH B:2143
BINDING SITE FOR RESIDUE SO4 B 604
16
BC7
SOFTWARE
THR B:97 , ASP B:102 , HIS B:282 , SER B:284 , HOH B:2030
BINDING SITE FOR RESIDUE SO4 B 605
17
BC8
SOFTWARE
GLU B:188 , HIS B:247 , GLU B:251
BINDING SITE FOR RESIDUE CO B 610
18
BC9
SOFTWARE
LEU B:63 , HIS B:67
BINDING SITE FOR RESIDUE CO B 612
19
CC1
SOFTWARE
HIS B:158
BINDING SITE FOR RESIDUE CO B 613
20
CC2
SOFTWARE
ALA C:48 , SER C:49 , TYR C:147 , SER C:298 , GLY C:412 , THR C:413 , HOH C:2146 , HOH C:2147
BINDING SITE FOR RESIDUE BIY C 500
21
CC3
SOFTWARE
HIS C:282 , THR C:283
BINDING SITE FOR RESIDUE SO4 C 601
22
CC4
SOFTWARE
ARG C:236
BINDING SITE FOR RESIDUE SO4 C 602
23
CC5
SOFTWARE
TRP C:139 , SER C:415
BINDING SITE FOR RESIDUE SO4 C 603
24
CC6
SOFTWARE
SER C:131 , GLU C:132 , ARG C:133 , LEU C:134
BINDING SITE FOR RESIDUE SO4 C 604
25
CC7
SOFTWARE
ASP C:95 , THR C:97 , ASP C:102 , HIS C:282 , HOH C:2030
BINDING SITE FOR RESIDUE SO4 C 605
26
CC8
SOFTWARE
GLU C:188 , HIS C:247 , GLU C:251
BINDING SITE FOR RESIDUE CO C 610
27
CC9
SOFTWARE
LEU C:63 , HIS C:67
BINDING SITE FOR RESIDUE CO C 612
28
DC1
SOFTWARE
HIS C:158 , GLU C:168 , HOH C:2148
BINDING SITE FOR RESIDUE CO C 613
29
DC2
SOFTWARE
ALA D:48 , SER D:49 , TYR D:147 , SER D:298 , ASN D:300 , GLY D:412 , THR D:413 , HOH D:2124
BINDING SITE FOR RESIDUE BIY D 500
30
DC3
SOFTWARE
HIS D:282 , THR D:283
BINDING SITE FOR RESIDUE SO4 D 601
31
DC4
SOFTWARE
ALA D:234 , ARG D:236
BINDING SITE FOR RESIDUE SO4 D 602
32
DC5
SOFTWARE
GLU D:141 , ASP D:211
BINDING SITE FOR RESIDUE SO4 D 603
33
DC6
SOFTWARE
SER D:131 , GLU D:132 , ARG D:133 , LEU D:134
BINDING SITE FOR RESIDUE SO4 D 604
34
DC7
SOFTWARE
ASP D:95 , THR D:97 , ASP D:102 , HIS D:282 , HOH D:2024
BINDING SITE FOR RESIDUE SO4 D 605
35
DC8
SOFTWARE
GLU D:188 , HIS D:247 , GLU D:251 , HOH D:2137
BINDING SITE FOR RESIDUE CO D 610
36
DC9
SOFTWARE
HIS D:462
BINDING SITE FOR RESIDUE CO D 611
37
EC1
SOFTWARE
LEU D:63 , HIS D:67
BINDING SITE FOR RESIDUE CO D 612
38
EC2
SOFTWARE
HIS D:158 , GLU D:168 , HOH D:2138
BINDING SITE FOR RESIDUE CO D 613
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
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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
(1, 4)
Info
All SCOP Domains
1a: SCOP_d2wkea_ (A:)
1b: SCOP_d2wkeb_ (B:)
1c: SCOP_d2wkec_ (C:)
1d: SCOP_d2wked_ (D:)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
beta-lactamase/transpeptidase-like
(515)
Superfamily
:
beta-lactamase/transpeptidase-like
(515)
Family
:
Dac-like
(29)
Protein domain
:
D-alanyl-D-alanine carboxypeptidase Dac
(17)
Actinomadura sp. [TaxId: 1989]
(17)
1a
d2wkea_
A:
1b
d2wkeb_
B:
1c
d2wkec_
C:
1d
d2wked_
D:
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_2wkeA01 (A:1-68,A:285-466)
1b: CATH_2wkeB01 (B:1-68,B:285-466)
1c: CATH_2wkeC01 (C:1-68,C:285-466)
1d: CATH_2wkeD01 (D:1-68,D:285-466)
View:
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Classes
(
)
(
)
Architectures
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)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Beta-lactamase
(339)
Homologous Superfamily
:
DD-peptidase/beta-lactamase superfamily
(335)
Actinomadura sp.. Organism_taxid: 72570. Strain: r39
(4)
1a
2wkeA01
A:1-68,A:285-466
1b
2wkeB01
B:1-68,B:285-466
1c
2wkeC01
C:1-68,C:285-466
1d
2wkeD01
D:1-68,D:285-466
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Label:
Sorry, no Info available
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select residue range 5 to 10 in chain 'A'
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Asym.Unit (295 KB)
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Biol.Unit 2 (75 KB)
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Biol.Unit 3 (75 KB)
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