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2Y55
Asym. Unit
Info
Asym.Unit (586 KB)
Biol.Unit 1 (148 KB)
Biol.Unit 2 (147 KB)
Biol.Unit 3 (147 KB)
Biol.Unit 4 (151 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) - 27 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
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
(4, 30)
Info
All Hetero Components
1a: ACETONE (ACNa)
1b: ACETONE (ACNb)
1c: ACETONE (ACNc)
1d: ACETONE (ACNd)
1e: ACETONE (ACNe)
2a: PHENYLACETAMIDOMETHYL BORONIC ACID (FP5a)
2b: PHENYLACETAMIDOMETHYL BORONIC ACID (FP5b)
2c: PHENYLACETAMIDOMETHYL BORONIC ACID (FP5c)
2d: PHENYLACETAMIDOMETHYL BORONIC ACID (FP5d)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
4e: SULFATE ION (SO4e)
4f: SULFATE ION (SO4f)
4g: SULFATE ION (SO4g)
4h: SULFATE ION (SO4h)
4i: SULFATE ION (SO4i)
4j: SULFATE ION (SO4j)
4k: SULFATE ION (SO4k)
4l: SULFATE ION (SO4l)
4m: SULFATE ION (SO4m)
4n: SULFATE ION (SO4n)
4o: SULFATE ION (SO4o)
4p: SULFATE ION (SO4p)
4q: SULFATE ION (SO4q)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACN
5
Ligand/Ion
ACETONE
2
FP5
4
Ligand/Ion
PHENYLACETAMIDOMETHYL BORONIC ACID
3
MG
4
Ligand/Ion
MAGNESIUM ION
4
SO4
17
Ligand/Ion
SULFATE ION
[
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Sites
(30, 30)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ALA A:48 , SER A:49 , LYS A:52 , SER A:298 , ASN A:300 , LYS A:410 , THR A:411 , GLY A:412 , THR A:413 , ACN A:1473
BINDING SITE FOR RESIDUE FP5 A 500
02
AC2
SOFTWARE
ASP A:281 , HIS A:282 , THR A:283
BINDING SITE FOR RESIDUE SO4 A1467
03
AC3
SOFTWARE
ALA A:234 , ARG A:236 , HOH A:2079
BINDING SITE FOR RESIDUE SO4 A1468
04
AC4
SOFTWARE
SER A:131 , GLU A:132 , ARG A:133 , LEU A:134
BINDING SITE FOR RESIDUE SO4 A1469
05
AC5
SOFTWARE
GLY A:159 , GLU A:160 , ARG A:161
BINDING SITE FOR RESIDUE SO4 A1470
06
AC6
SOFTWARE
GLU A:188 , HIS A:247 , GLU A:251
BINDING SITE FOR RESIDUE MG A1471
07
AC7
SOFTWARE
VAL A:406 , HIS A:462
BINDING SITE FOR RESIDUE MG A1472
08
AC8
SOFTWARE
TYR A:147 , THR A:413 , MET A:414 , FP5 A:500
BINDING SITE FOR RESIDUE ACN A1473
09
AC9
SOFTWARE
ARG A:161
BINDING SITE FOR RESIDUE SO4 A1474
10
BC1
SOFTWARE
ALA B:48 , SER B:49 , LYS B:52 , SER B:298 , ASN B:300 , SER B:347 , GLY B:348 , LEU B:349 , LYS B:410 , THR B:411 , GLY B:412 , THR B:413 , ACN B:1471
BINDING SITE FOR RESIDUE FP5 B 500
11
BC2
SOFTWARE
ASP B:281 , HIS B:282 , THR B:283
BINDING SITE FOR RESIDUE SO4 B1467
12
BC3
SOFTWARE
ALA B:234 , ARG B:236 , HOH B:2068
BINDING SITE FOR RESIDUE SO4 B1468
13
BC4
SOFTWARE
SER B:131 , GLU B:132 , ARG B:133 , LEU B:134
BINDING SITE FOR RESIDUE SO4 B1469
14
BC5
SOFTWARE
HIS B:158 , GLY B:159 , GLU B:160 , ARG B:161
BINDING SITE FOR RESIDUE SO4 B1470
15
BC6
SOFTWARE
THR B:413 , FP5 B:500
BINDING SITE FOR RESIDUE ACN B1471
16
BC7
SOFTWARE
ALA C:48 , SER C:49 , LYS C:52 , SER C:298 , ASN C:300 , GLY C:348 , LYS C:410 , GLY C:412 , THR C:413
BINDING SITE FOR RESIDUE FP5 C 500
17
BC8
SOFTWARE
ASP C:281 , HIS C:282 , THR C:283 , HOH C:2064
BINDING SITE FOR RESIDUE SO4 C1467
18
BC9
SOFTWARE
ARG C:236
BINDING SITE FOR RESIDUE SO4 C1468
19
CC1
SOFTWARE
SER C:131 , ARG C:133 , LEU C:134
BINDING SITE FOR RESIDUE SO4 C1469
20
CC2
SOFTWARE
GLY C:159 , GLU C:160 , ARG C:161
BINDING SITE FOR RESIDUE SO4 C1470
21
CC3
SOFTWARE
THR C:413
BINDING SITE FOR RESIDUE ACN C1471
22
CC4
SOFTWARE
SER D:49 , LYS D:52 , SER D:298 , ASN D:300 , LYS D:410 , THR D:411 , THR D:413 , MET D:414 , ACN D:1473
BINDING SITE FOR RESIDUE FP5 D 500
23
CC5
SOFTWARE
ASP D:281 , HIS D:282 , THR D:283 , HOH D:2034
BINDING SITE FOR RESIDUE SO4 D1467
24
CC6
SOFTWARE
ALA D:234 , ARG D:236
BINDING SITE FOR RESIDUE SO4 D1468
25
CC7
SOFTWARE
SER D:131 , GLU D:132 , ARG D:133 , LEU D:134
BINDING SITE FOR RESIDUE SO4 D1469
26
CC8
SOFTWARE
GLY D:159 , GLU D:160 , ARG D:161
BINDING SITE FOR RESIDUE SO4 D1470
27
CC9
SOFTWARE
GLU D:188 , HIS D:247 , GLU D:251
BINDING SITE FOR RESIDUE MG D1471
28
DC1
SOFTWARE
HIS D:462
BINDING SITE FOR RESIDUE MG D1472
29
DC2
SOFTWARE
ASP D:142 , TYR D:147 , LEU D:349 , MET D:414 , FP5 D:500
BINDING SITE FOR RESIDUE ACN D1473
30
DC3
SOFTWARE
THR D:127 , GLY D:318
BINDING SITE FOR RESIDUE ACN D1474
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
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Exons
(0, 0)
Info
All 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
(1, 4)
Info
All SCOP Domains
1a: SCOP_d2y55a_ (A:)
1b: SCOP_d2y55b_ (B:)
1c: SCOP_d2y55c_ (C:)
1d: SCOP_d2y55d_ (D:)
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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
d2y55a_
A:
1b
d2y55b_
B:
1c
d2y55c_
C:
1d
d2y55d_
D:
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CATH Domains
(0, 0)
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all CATH domains
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Sorry, no Info available
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Pfam Domains
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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 (586 KB)
Header - Asym.Unit
Biol.Unit 1 (148 KB)
Header - Biol.Unit 1
Biol.Unit 2 (147 KB)
Header - Biol.Unit 2
Biol.Unit 3 (147 KB)
Header - Biol.Unit 3
Biol.Unit 4 (151 KB)
Header - Biol.Unit 4
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