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2Y59
Asym. Unit
Info
Asym.Unit (580 KB)
Biol.Unit 1 (146 KB)
Biol.Unit 2 (146 KB)
Biol.Unit 3 (146 KB)
Biol.Unit 4 (149 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
:
12 Jan 11 (Deposition) - 27 Jul 11 (Release) - 12 Jul 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
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-Inhibitor Complex, Peptidoglycan, Hydrolase
(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
(3, 29)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
1c: MAGNESIUM ION (MGc)
1d: MAGNESIUM ION (MGd)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
2e: SULFATE ION (SO4e)
2f: SULFATE ION (SO4f)
2g: SULFATE ION (SO4g)
2h: SULFATE ION (SO4h)
2i: SULFATE ION (SO4i)
2j: SULFATE ION (SO4j)
2k: SULFATE ION (SO4k)
2l: SULFATE ION (SO4l)
2m: SULFATE ION (SO4m)
2n: SULFATE ION (SO4n)
2o: SULFATE ION (SO4o)
2p: SULFATE ION (SO4p)
2q: SULFATE ION (SO4q)
2r: SULFATE ION (SO4r)
2s: SULFATE ION (SO4s)
2t: SULFATE ION (SO4t)
2u: SULFATE ION (SO4u)
3a: TRIHYDROXY-[[(2-NITROPHENYL)CARBON... (ZA3a)
3b: TRIHYDROXY-[[(2-NITROPHENYL)CARBON... (ZA3b)
3c: TRIHYDROXY-[[(2-NITROPHENYL)CARBON... (ZA3c)
3d: TRIHYDROXY-[[(2-NITROPHENYL)CARBON... (ZA3d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
4
Ligand/Ion
MAGNESIUM ION
2
SO4
21
Ligand/Ion
SULFATE ION
3
ZA3
4
Ligand/Ion
TRIHYDROXY-[[(2-NITROPHENYL)CARBONYLAMINO]METHYL]BORON
[
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Sites
(29, 29)
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)
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 , LEU A:349 , GLY A:412 , THR A:413 , SO4 A:502 , ALA B:175 , GLU B:176
BINDING SITE FOR RESIDUE ZA3 A 500
02
AC2
SOFTWARE
SER A:49 , SER A:298 , THR A:393 , LYS A:410 , THR A:411 , GLY A:412 , THR A:413 , ZA3 A:501
BINDING SITE FOR RESIDUE SO4 A 1467
03
AC3
SOFTWARE
ASP A:281 , HIS A:282 , THR A:283
BINDING SITE FOR RESIDUE SO4 A 1468
04
AC4
SOFTWARE
ARG A:236 , HOH A:624
BINDING SITE FOR RESIDUE SO4 A 1469
05
AC5
SOFTWARE
SER A:131 , ARG A:133 , LEU A:134
BINDING SITE FOR RESIDUE SO4 A 1470
06
AC6
SOFTWARE
GLY A:159 , GLU A:160 , ARG A:161 , HOH A:640
BINDING SITE FOR RESIDUE SO4 A 1471
07
AC7
SOFTWARE
GLU A:188 , HIS A:247 , GLU A:251
BINDING SITE FOR RESIDUE MG A 1472
08
AC8
SOFTWARE
ALA A:402 , VAL A:406 , HIS A:462
BINDING SITE FOR RESIDUE MG A 1473
09
AC9
SOFTWARE
ALA B:48 , SER B:49 , LYS B:52 , TYR B:147 , SER B:298 , LYS B:410 , THR B:411 , GLY B:412 , THR B:413 , MET B:414 , HOH B:606 , HOH B:639
BINDING SITE FOR RESIDUE ZA3 B 500
10
BC1
SOFTWARE
HIS B:282 , THR B:283
BINDING SITE FOR RESIDUE SO4 B 1467
11
BC2
SOFTWARE
ALA B:234 , ARG B:236 , HOH B:644 , HOH B:679
BINDING SITE FOR RESIDUE SO4 B 1468
12
BC3
SOFTWARE
SER B:131 , GLU B:132 , ARG B:133 , LEU B:134 , HOH B:661
BINDING SITE FOR RESIDUE SO4 B 1469
13
BC4
SOFTWARE
GLY B:159 , GLU B:160 , ARG B:161
BINDING SITE FOR RESIDUE SO4 B 1470
14
BC5
SOFTWARE
TRP B:139 , SER B:415
BINDING SITE FOR RESIDUE SO4 B 1471
15
BC6
SOFTWARE
ALA C:48 , SER C:49 , LYS C:52 , SER C:298 , LYS C:410 , GLY C:412 , THR C:413 , MET C:414 , HOH C:625
BINDING SITE FOR RESIDUE ZA3 C 500
16
BC7
SOFTWARE
ASP C:281 , HIS C:282 , THR C:283
BINDING SITE FOR RESIDUE SO4 C 1467
17
BC8
SOFTWARE
ALA C:234 , ARG C:236
BINDING SITE FOR RESIDUE SO4 C 1468
18
BC9
SOFTWARE
SER C:131 , GLU C:132 , ARG C:133 , LEU C:134
BINDING SITE FOR RESIDUE SO4 C 1469
19
CC1
SOFTWARE
GLY C:159 , GLU C:160 , ARG C:161 , HOH C:607
BINDING SITE FOR RESIDUE SO4 C 1470
20
CC2
SOFTWARE
TRP C:139 , SER C:415 , HOH C:622 , HOH C:610
BINDING SITE FOR RESIDUE SO4 C 1471
21
CC3
SOFTWARE
GLU D:430 , HOH D:2001
BINDING SITE FOR RESIDUE SO4 C 1472
22
CC4
SOFTWARE
ALA D:48 , SER D:49 , TYR D:147 , SER D:298 , ASN D:300 , LEU D:349 , GLY D:412 , THR D:413 , SO4 D:503
BINDING SITE FOR RESIDUE ZA3 D 500
23
CC5
SOFTWARE
SER D:49 , SER D:298 , THR D:393 , LYS D:410 , THR D:411 , GLY D:412 , THR D:413 , ZA3 D:502 , HOH D:2010
BINDING SITE FOR RESIDUE SO4 D 1467
24
CC6
SOFTWARE
ASP D:281 , HIS D:282 , THR D:283 , HOH D:2003 , HOH D:2017
BINDING SITE FOR RESIDUE SO4 D 1468
25
CC7
SOFTWARE
ALA D:234 , ARG D:236
BINDING SITE FOR RESIDUE SO4 D 1469
26
CC8
SOFTWARE
SER D:131 , ARG D:133 , LEU D:134 , HOH D:2037
BINDING SITE FOR RESIDUE SO4 D 1470
27
CC9
SOFTWARE
GLY D:159 , GLU D:160 , ARG D:161
BINDING SITE FOR RESIDUE SO4 D 1471
28
DC1
SOFTWARE
ALA D:186 , GLU D:188 , HIS D:247 , GLU D:251
BINDING SITE FOR RESIDUE MG D 1472
29
DC2
SOFTWARE
VAL D:406 , HIS D:462
BINDING SITE FOR RESIDUE MG D 1473
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
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End label:
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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.
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d2y59a_ (A:)
1b: SCOP_d2y59b_ (B:)
1c: SCOP_d2y59c_ (C:)
1d: SCOP_d2y59d_ (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
d2y59a_
A:
1b
d2y59b_
B:
1c
d2y59c_
C:
1d
d2y59d_
D:
[
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(0, 0)
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Sorry, no Info available
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Chain D
Asymmetric Unit 1
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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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Asym.Unit (580 KB)
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Biol.Unit 1 (146 KB)
Header - Biol.Unit 1
Biol.Unit 2 (146 KB)
Header - Biol.Unit 2
Biol.Unit 3 (146 KB)
Header - Biol.Unit 3
Biol.Unit 4 (149 KB)
Header - Biol.Unit 4
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