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2XK1
Biol. Unit 1
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:
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Gene Ontology, PubMed, Web (Google)
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)
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
(2, 5)
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:
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No.
Name
Count
Type
Full Name
1
CO
-1
Ligand/Ion
COBALT (II) ION
2
EWB
1
Ligand/Ion
[(1S)-1-{[(2-BENZYLPHENYL)CARBONYL]AMINO}ETHYL](TRIHYDROXY)BORATE(1-)
3
SO4
4
Ligand/Ion
SULFATE ION
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Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC5 (SOFTWARE)
3: AC6 (SOFTWARE)
4: AC7 (SOFTWARE)
5: AC8 (SOFTWARE)
6: AC9 (SOFTWARE)
7: BC1 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
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
2
AC5
SOFTWARE
HIS A:282 , THR A:283
BINDING SITE FOR RESIDUE SO4 A 601
3
AC6
SOFTWARE
ALA A:234 , LEU A:235 , ARG A:236 , HOH A:2054
BINDING SITE FOR RESIDUE SO4 A 602
4
AC7
SOFTWARE
SER A:131 , GLU A:132 , ARG A:133 , LEU A:134 , HOH A:2056
BINDING SITE FOR RESIDUE SO4 A 603
5
AC8
SOFTWARE
GLY A:159 , GLU A:160 , ARG A:161 , HOH A:2058
BINDING SITE FOR RESIDUE SO4 A 604
6
AC9
SOFTWARE
GLU A:188 , HIS A:247 , GLU A:251 , GLU A:466
BINDING SITE FOR RESIDUE CO A 610
7
BC1
SOFTWARE
ASP A:181 , ASP A:183 , VAL A:406 , HIS A:462
BINDING SITE FOR RESIDUE CO A 611
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
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Exons
(0, 0)
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
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
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Organisms
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)
(
)
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
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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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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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Chain A
Asymmetric Unit 1
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Asym.Unit (581 KB)
Header - Asym.Unit
Biol.Unit 1 (147 KB)
Header - Biol.Unit 1
Biol.Unit 2 (147 KB)
Header - Biol.Unit 2
Biol.Unit 3 (147 KB)
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Biol.Unit 4 (147 KB)
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