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2XK1
Asym. Unit
Info
Asym.Unit (581 KB)
Biol.Unit 1 (147 KB)
Biol.Unit 2 (147 KB)
Biol.Unit 3 (147 KB)
Biol.Unit 4 (147 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF A COMPLEX BETWEEN ACTINOMADURA R39 DD-PEPTIDASE AND A BORONATE INHIBITOR
Authors
:
E. Sauvage, R. Herman, F. Kerff, M. Rocaboy, P. Charlier
Date
:
07 Jul 10 (Deposition) - 26 Jan 11 (Release) - 18 Jun 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
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
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. C. Y. Woon, A. Zervosen, E. Sauvage, K. J. Simmons, M. Ivec, S. R. Inglis, C. W. G. Fishwick, S. Gobec, P. Charlier, A. Luxen, C. J. Schofield
Structure Guided Development Of Potent Reversibly Binding Penicillin Binding Protein Inhibitors
Acs Med. Chem. Lett. V. 2 219 2011
[
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Hetero Components
(3, 24)
Info
All Hetero Components
1a: COBALT (II) ION (COa)
1b: COBALT (II) ION (COb)
1c: COBALT (II) ION (COc)
1d: COBALT (II) ION (COd)
2a: [(1S)-1-{[(2-BENZYLPHENYL)CARBONYL... (EWBa)
2b: [(1S)-1-{[(2-BENZYLPHENYL)CARBONYL... (EWBb)
2c: [(1S)-1-{[(2-BENZYLPHENYL)CARBONYL... (EWBc)
2d: [(1S)-1-{[(2-BENZYLPHENYL)CARBONYL... (EWBd)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CO
4
Ligand/Ion
COBALT (II) ION
2
EWB
4
Ligand/Ion
[(1S)-1-{[(2-BENZYLPHENYL)CARBONYL]AMINO}ETHYL](TRIHYDROXY)BORATE(1-)
3
SO4
16
Ligand/Ion
SULFATE ION
[
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Sites
(24, 24)
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)
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 , ALA C:175 , GLU C:176 , GLU C:178
BINDING SITE FOR RESIDUE EWB A 500
02
AC2
SOFTWARE
SER B:49 , LYS B:52 , TYR B:147 , SER B:298 , ASN B:300 , GLY B:348 , GLY B:412 , THR B:413
BINDING SITE FOR RESIDUE EWB B 500
03
AC3
SOFTWARE
ALA C:48 , SER C:49 , LYS C:52 , TYR C:147 , SER C:298 , ASN C:300 , GLY C:412 , THR C:413
BINDING SITE FOR RESIDUE EWB C 500
04
AC4
SOFTWARE
GLU B:176 , ALA D:48 , SER D:49 , TYR D:147 , SER D:298 , ASN D:300 , LEU D:349 , GLY D:412 , THR D:413
BINDING SITE FOR RESIDUE EWB D 500
05
AC5
SOFTWARE
HIS A:282 , THR A:283
BINDING SITE FOR RESIDUE SO4 A 601
06
AC6
SOFTWARE
ALA A:234 , LEU A:235 , ARG A:236 , HOH A:2054
BINDING SITE FOR RESIDUE SO4 A 602
07
AC7
SOFTWARE
SER A:131 , GLU A:132 , ARG A:133 , LEU A:134 , HOH A:2056
BINDING SITE FOR RESIDUE SO4 A 603
08
AC8
SOFTWARE
GLY A:159 , GLU A:160 , ARG A:161 , HOH A:2058
BINDING SITE FOR RESIDUE SO4 A 604
09
AC9
SOFTWARE
GLU A:188 , HIS A:247 , GLU A:251 , GLU A:466
BINDING SITE FOR RESIDUE CO A 610
10
BC1
SOFTWARE
ASP A:181 , ASP A:183 , VAL A:406 , HIS A:462
BINDING SITE FOR RESIDUE CO A 611
11
BC2
SOFTWARE
HIS B:282 , THR B:283
BINDING SITE FOR RESIDUE SO4 B 601
12
BC3
SOFTWARE
TYR B:145 , ALA B:234 , ARG B:236 , HOH B:2039
BINDING SITE FOR RESIDUE SO4 B 602
13
BC4
SOFTWARE
SER B:131 , GLU B:132 , ARG B:133 , LEU B:134
BINDING SITE FOR RESIDUE SO4 B 603
14
BC5
SOFTWARE
GLY B:159 , GLU B:160 , ARG B:161
BINDING SITE FOR RESIDUE SO4 B 604
15
BC6
SOFTWARE
ASP C:281 , HIS C:282 , THR C:283
BINDING SITE FOR RESIDUE SO4 C 601
16
BC7
SOFTWARE
ALA C:234 , ARG C:236 , HOH C:2041
BINDING SITE FOR RESIDUE SO4 C 602
17
BC8
SOFTWARE
SER C:131 , GLU C:132 , ARG C:133 , LEU C:134
BINDING SITE FOR RESIDUE SO4 C 603
18
BC9
SOFTWARE
HIS C:158 , GLY C:159 , GLU C:160 , ARG C:161
BINDING SITE FOR RESIDUE SO4 C 604
19
CC1
SOFTWARE
HIS D:282 , THR D:283
BINDING SITE FOR RESIDUE SO4 D 601
20
CC2
SOFTWARE
ALA D:234 , LEU D:235 , ARG D:236
BINDING SITE FOR RESIDUE SO4 D 602
21
CC3
SOFTWARE
GLU D:132 , ARG D:133 , LEU D:134
BINDING SITE FOR RESIDUE SO4 D 603
22
CC4
SOFTWARE
GLY D:159 , GLU D:160 , ARG D:161
BINDING SITE FOR RESIDUE SO4 D 604
23
CC5
SOFTWARE
GLU D:188 , HIS D:247 , GLU D:251 , GLU D:466
BINDING SITE FOR RESIDUE CO D 610
24
CC6
SOFTWARE
ASP D:181 , ASP D:183 , VAL D:406 , HIS D:462
BINDING SITE FOR RESIDUE CO D 611
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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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;
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Sorry, no Info available
[
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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_d2xk1a_ (A:)
1b: SCOP_d2xk1b_ (B:)
1c: SCOP_d2xk1c_ (C:)
1d: SCOP_d2xk1d_ (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
d2xk1a_
A:
1b
d2xk1b_
B:
1c
d2xk1c_
C:
1d
d2xk1d_
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
(1, 4)
Info
all PFAM domains
1a: PFAM_Peptidase_S13_2xk1D01 (D:5-459)
1b: PFAM_Peptidase_S13_2xk1D02 (D:5-459)
1c: PFAM_Peptidase_S13_2xk1D03 (D:5-459)
1d: PFAM_Peptidase_S13_2xk1D04 (D:5-459)
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Clans
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(
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Organisms
(
)
(
)
Clan
:
Beta-lactamase
(210)
Family
:
Peptidase_S13
(9)
Actinomadura sp. (strain R39)
(8)
1a
Peptidase_S13-2xk1D01
D:5-459
1b
Peptidase_S13-2xk1D02
D:5-459
1c
Peptidase_S13-2xk1D03
D:5-459
1d
Peptidase_S13-2xk1D04
D:5-459
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Asym.Unit (581 KB)
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Biol.Unit 3 (147 KB)
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