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Asym. Unit
Info
Asym.Unit (633 KB)
Biol.Unit 1 (161 KB)
Biol.Unit 2 (160 KB)
Biol.Unit 3 (162 KB)
Biol.Unit 4 (160 KB)
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(1)
Title
:
UNEXPECTED TRICOVALENT BINDING MODE OF BORONIC ACIDS WITHIN THE ACTIVE SITE OF A PENICILLIN BINDING PROTEIN
Authors
:
E. Sauvage, A. Zervosen, R. Herman, F. Kerff, M. Rocaboy, P. Charlier
Date
:
28 Jul 11 (Deposition) - 29 Feb 12 (Release) - 29 Feb 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
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, Peptidoglycan, Penicillin-Binding, Tetravalent Boron
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Zervosen, R. Herman, F. Kerff, A. Herman, A. Bouillez, F. Prati, R. F. Pratt, J. M. Frere, B. Joris, A. Luxen, P. Charlier, E. Sauvage
Unexpected Tricovalent Binding Mode Of Boronic Acids Within The Active Site Of A Penicillin- Binding Protein.
J. Am. Chem. Soc. V. 133 10839 2011
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Hetero Components
(6, 39)
Info
All Hetero Components
1a: 3,3-DIMETHYLBUTAN-1-OL (33Da)
1b: 3,3-DIMETHYLBUTAN-1-OL (33Db)
2a: ACETONE (ACNa)
2b: ACETONE (ACNb)
3a: PHENYLACETAMIDOMETHYL BORONIC ACID (FP5a)
3b: PHENYLACETAMIDOMETHYL BORONIC ACID (FP5b)
4a: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESa)
5a: MAGNESIUM ION (MGa)
5b: MAGNESIUM ION (MGb)
5c: MAGNESIUM ION (MGc)
5d: MAGNESIUM ION (MGd)
5e: MAGNESIUM ION (MGe)
5f: MAGNESIUM ION (MGf)
5g: MAGNESIUM ION (MGg)
5h: MAGNESIUM ION (MGh)
5i: MAGNESIUM ION (MGi)
5j: MAGNESIUM ION (MGj)
5k: MAGNESIUM ION (MGk)
5l: MAGNESIUM ION (MGl)
5m: MAGNESIUM ION (MGm)
5n: MAGNESIUM ION (MGn)
6a: SULFATE ION (SO4a)
6b: SULFATE ION (SO4b)
6c: SULFATE ION (SO4c)
6d: SULFATE ION (SO4d)
6e: SULFATE ION (SO4e)
6f: SULFATE ION (SO4f)
6g: SULFATE ION (SO4g)
6h: SULFATE ION (SO4h)
6i: SULFATE ION (SO4i)
6j: SULFATE ION (SO4j)
6k: SULFATE ION (SO4k)
6l: SULFATE ION (SO4l)
6m: SULFATE ION (SO4m)
6n: SULFATE ION (SO4n)
6o: SULFATE ION (SO4o)
6p: SULFATE ION (SO4p)
6q: SULFATE ION (SO4q)
6r: SULFATE ION (SO4r)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
33D
2
Ligand/Ion
3,3-DIMETHYLBUTAN-1-OL
2
ACN
2
Ligand/Ion
ACETONE
3
FP5
2
Ligand/Ion
PHENYLACETAMIDOMETHYL BORONIC ACID
4
MES
1
Ligand/Ion
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
5
MG
14
Ligand/Ion
MAGNESIUM ION
6
SO4
18
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(35, 35)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER A:49 , SER A:298 , THR A:393 , LYS A:410 , THR A:411 , GLY A:412 , THR A:413 , HOH A:2049 , HOH A:2448 , HOH A:2474
BINDING SITE FOR RESIDUE SO4 A 600
02
AC2
SOFTWARE
HIS A:282 , THR A:283 , HOH A:2151 , HOH A:2152 , HOH A:2359 , HOH A:2361
BINDING SITE FOR RESIDUE SO4 A 601
03
AC3
SOFTWARE
ALA A:234 , ARG A:236 , HOH A:2475
BINDING SITE FOR RESIDUE SO4 A 602
04
AC4
SOFTWARE
SER A:131 , ARG A:133 , LEU A:134 , HOH A:2231
BINDING SITE FOR RESIDUE SO4 A 603
05
AC5
SOFTWARE
GLY A:159 , GLU A:160 , ARG A:161 , HOH A:2238 , HOH A:2479
BINDING SITE FOR RESIDUE SO4 A 604
06
AC6
SOFTWARE
ALA A:186 , GLU A:188 , HIS A:247 , GLU A:251
BINDING SITE FOR RESIDUE MG A 610
07
AC7
SOFTWARE
ALA A:402 , VAL A:406 , HIS A:462 , GLN A:463 , HOH A:2441
BINDING SITE FOR RESIDUE MG A 611
08
AC8
SOFTWARE
HOH A:2080
BINDING SITE FOR RESIDUE MG A1469
09
AC9
SOFTWARE
ALA B:48 , SER B:49 , SER B:298 , ASN B:300 , GLY B:348 , LEU B:349 , LYS B:410 , THR B:411 , GLY B:412 , THR B:413 , HOH B:2442
BINDING SITE FOR RESIDUE FP5 B 500
10
BC1
SOFTWARE
HIS B:282 , THR B:283 , HOH B:2178 , HOH B:2366
BINDING SITE FOR RESIDUE SO4 B 601
11
BC2
SOFTWARE
ARG B:236 , HOH B:2473 , HOH B:2474
BINDING SITE FOR RESIDUE SO4 B 602
12
BC3
SOFTWARE
SER B:131 , ARG B:133 , LEU B:134 , HOH B:2209 , HOH B:2252 , HOH B:2476
BINDING SITE FOR RESIDUE SO4 B 603
13
BC4
SOFTWARE
GLY B:159 , GLU B:160 , ARG B:161 , HOH B:2262 , HOH B:2264 , HOH B:2269 , HOH B:2478
BINDING SITE FOR RESIDUE SO4 B 604
14
BC5
SOFTWARE
HOH B:2480 , TRP C:139 , ARG C:351 , MET C:414 , SER C:415 , HOH C:2489
BINDING SITE FOR RESIDUE 33D B 620
15
BC6
SOFTWARE
HOH B:2481
BINDING SITE FOR RESIDUE MG B1467
16
BC7
SOFTWARE
ASP B:40
BINDING SITE FOR RESIDUE MG B3001
17
BC8
SOFTWARE
ALA C:48 , SER C:49 , SER C:298 , ASN C:300 , GLY C:348 , LEU C:349 , LYS C:410 , THR C:411 , GLY C:412 , THR C:413 , ACN C:610 , HOH C:2484
BINDING SITE FOR RESIDUE FP5 C 500
18
BC9
SOFTWARE
HIS C:282 , THR C:283 , HOH C:2185 , HOH C:2397 , HOH C:2400
BINDING SITE FOR RESIDUE SO4 C 601
19
CC1
SOFTWARE
ARG C:236 , HOH C:2523
BINDING SITE FOR RESIDUE SO4 C 602
20
CC2
SOFTWARE
SER C:131 , GLU C:132 , ARG C:133 , LEU C:134 , HOH C:2216 , HOH C:2222 , HOH C:2261 , HOH C:2525
BINDING SITE FOR RESIDUE SO4 C 603
21
CC3
SOFTWARE
HIS C:158 , GLY C:159 , GLU C:160 , ARG C:161 , HOH C:2270 , HOH C:2278 , HOH C:2528
BINDING SITE FOR RESIDUE SO4 C 604
22
CC4
SOFTWARE
THR C:413 , FP5 C:500 , HOH C:2242 , HOH C:2529
BINDING SITE FOR RESIDUE ACN C 610
23
CC5
SOFTWARE
TRP B:139 , MET B:414 , SER B:415
BINDING SITE FOR RESIDUE 33D C 620
24
CC6
SOFTWARE
ARG C:455
BINDING SITE FOR RESIDUE MG C1467
25
CC7
SOFTWARE
VAL C:214
BINDING SITE FOR RESIDUE MG C1468
26
CC8
SOFTWARE
GLN C:312 , GLY C:316
BINDING SITE FOR RESIDUE MG C1469
27
CC9
SOFTWARE
ASP C:40
BINDING SITE FOR RESIDUE MG C3001
28
DC1
SOFTWARE
SER D:49 , SER D:298 , THR D:393 , LYS D:410 , THR D:411 , GLY D:412 , THR D:413 , HOH D:2066 , HOH D:2436
BINDING SITE FOR RESIDUE SO4 D 600
29
DC2
SOFTWARE
HIS D:282 , THR D:283 , HOH D:2338 , HOH D:2339
BINDING SITE FOR RESIDUE SO4 D 601
30
DC3
SOFTWARE
ALA D:234 , ARG D:236 , HOH D:2308 , HOH D:2461
BINDING SITE FOR RESIDUE SO4 D 602
31
DC4
SOFTWARE
SER D:131 , GLU D:132 , ARG D:133 , LEU D:134 , HOH D:2186 , HOH D:2229
BINDING SITE FOR RESIDUE SO4 D 603
32
DC5
SOFTWARE
GLY D:159 , GLU D:160 , ARG D:161 , HOH D:2237 , HOH D:2243 , HOH D:2463
BINDING SITE FOR RESIDUE SO4 D 604
33
DC6
SOFTWARE
ALA D:186 , GLU D:188 , GLU D:251
BINDING SITE FOR RESIDUE MG D 610
34
DC7
SOFTWARE
VAL D:406 , HIS D:462
BINDING SITE FOR RESIDUE MG D 611
35
DC8
SOFTWARE
GLY D:368 , GLN D:374 , TRP D:376 , SER D:377 , GLU D:408 , TYR D:423 , GLU D:430
BINDING SITE FOR RESIDUE MES D1469
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
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End label:
Sorry, no Info available
[
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Exons
(0, 0)
Info
All Exons
View:
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All Exon Boundaries
View:
Label:
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_d3zvwa_ (A:)
1b: SCOP_d3zvwb_ (B:)
1c: SCOP_d3zvwc_ (C:)
1d: SCOP_d3zvwd_ (D:)
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(
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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
d3zvwa_
A:
1b
d3zvwb_
B:
1c
d3zvwc_
C:
1d
d3zvwd_
D:
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Asym.Unit (633 KB)
Header - Asym.Unit
Biol.Unit 1 (161 KB)
Header - Biol.Unit 1
Biol.Unit 2 (160 KB)
Header - Biol.Unit 2
Biol.Unit 3 (162 KB)
Header - Biol.Unit 3
Biol.Unit 4 (160 KB)
Header - Biol.Unit 4
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