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1W79
Asym. Unit
Info
Asym.Unit (313 KB)
Biol.Unit 1 (81 KB)
Biol.Unit 2 (81 KB)
Biol.Unit 3 (82 KB)
Biol.Unit 4 (81 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE DD-TRANSPEPTIDASE-CARBOXYPEPTIDASE FROM ACTINOMADURA R39
Authors
:
E. Sauvage, R. Herman, S. Petrella, C. Duez, J. M. Frere, P. Charlier
Date
:
31 Aug 04 (Deposition) - 28 Jun 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
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
:
Penicillin-Binding, Peptidoglycan, Actinomadura, Transpeptidase, Antibiotic Resistance, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Sauvage, R. Herman, S. Petrella, C. Duez, F. Bouillenne, J. M. Frere, P. Charlier
Crystal Structure Of The Actinomadura R39 Dd- Peptidase Reveals New Domains In Penicillin- Binding Proteins.
J. Biol. Chem. V. 280 31249 2005
(for further references see the
PDB file header
)
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Hetero Components
(2, 16)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
4
Ligand/Ion
MAGNESIUM ION
2
SO4
12
Ligand/Ion
SULFATE ION
[
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Sites
(16, 16)
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)
View:
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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:2045 , HOH A:2430 , HOH A:2431 , HOH A:2432
BINDING SITE FOR RESIDUE SO4 A 500
02
AC2
SOFTWARE
HIS A:282 , THR A:283 , HOH A:2282 , HOH A:2285 , HOH A:2286 , HOH A:2433
BINDING SITE FOR RESIDUE SO4 A 501
03
AC3
SOFTWARE
ALA A:234 , ARG A:236 , HOH A:2252 , HOH A:2434 , HOH A:2435 , HOH A:2436 , HOH A:2437 , HOH A:2438
BINDING SITE FOR RESIDUE SO4 A 502
04
AC4
SOFTWARE
GLU A:188 , HIS A:247 , GLU A:251
BINDING SITE FOR RESIDUE MG A 510
05
AC5
SOFTWARE
VAL A:406 , HIS A:462
BINDING SITE FOR RESIDUE MG A 511
06
AC6
SOFTWARE
SER B:49 , SER B:298 , LYS B:410 , THR B:411 , GLY B:412 , THR B:413 , HOH B:2418 , HOH B:2457 , HOH B:2458 , HOH B:2459 , HOH B:2460
BINDING SITE FOR RESIDUE SO4 B 500
07
AC7
SOFTWARE
ASP B:281 , HIS B:282 , THR B:283 , HOH B:2312 , HOH B:2316
BINDING SITE FOR RESIDUE SO4 B 501
08
AC8
SOFTWARE
ARG B:236 , HOH B:2272 , HOH B:2461
BINDING SITE FOR RESIDUE SO4 B 502
09
AC9
SOFTWARE
SER C:49 , SER C:298 , THR C:393 , LYS C:410 , THR C:411 , GLY C:412 , THR C:413 , HOH C:2045 , HOH C:2457 , HOH C:2458
BINDING SITE FOR RESIDUE SO4 C 500
10
BC1
SOFTWARE
ASP C:281 , HIS C:282 , THR C:283 , HOH C:2317 , HOH C:2459 , HOH C:2460
BINDING SITE FOR RESIDUE SO4 C 501
11
BC2
SOFTWARE
ARG C:236 , HOH C:2461 , HOH C:2462 , HOH C:2463 , HOH C:2464
BINDING SITE FOR RESIDUE SO4 C 502
12
BC3
SOFTWARE
SER D:49 , SER D:298 , THR D:393 , LYS D:410 , THR D:411 , GLY D:412 , THR D:413 , HOH D:2036 , HOH D:2410 , HOH D:2411 , HOH D:2412 , HOH D:2413
BINDING SITE FOR RESIDUE SO4 D 500
13
BC4
SOFTWARE
HIS D:282 , THR D:283 , HOH D:2282 , HOH D:2283 , HOH D:2414 , HOH D:2415 , HOH D:2416
BINDING SITE FOR RESIDUE SO4 D 501
14
BC5
SOFTWARE
ALA D:234 , ARG D:236 , HOH D:2241 , HOH D:2417
BINDING SITE FOR RESIDUE SO4 D 502
15
BC6
SOFTWARE
MG D:511
BINDING SITE FOR RESIDUE MG D 510
16
BC7
SOFTWARE
MG D:510
BINDING SITE FOR RESIDUE MG D 511
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
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Exons
(0, 0)
Info
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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_d1w79a1 (A:1-467)
1b: SCOP_d1w79b1 (B:1-466)
1c: SCOP_d1w79c1 (C:1-466)
1d: SCOP_d1w79d1 (D:1-467)
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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
d1w79a1
A:1-467
1b
d1w79b1
B:1-466
1c
d1w79c1
C:1-466
1d
d1w79d1
D:1-467
[
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1w79A01 (A:1-68,A:285-467)
1b: CATH_1w79D01 (D:1-68,D:285-467)
1c: CATH_1w79B01 (B:1-68,B:285-466)
1d: CATH_1w79C01 (C:1-68,C:285-466)
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Beta-lactamase
(339)
Homologous Superfamily
:
DD-peptidase/beta-lactamase superfamily
(335)
[unclassified]
(3)
1a
1w79A01
A:1-68,A:285-467
1b
1w79D01
D:1-68,D:285-467
1c
1w79B01
B:1-68,B:285-466
1d
1w79C01
C:1-68,C:285-466
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Peptidase_S13_1w79D01 (D:5-459)
1b: PFAM_Peptidase_S13_1w79D02 (D:5-459)
1c: PFAM_Peptidase_S13_1w79D03 (D:5-459)
1d: PFAM_Peptidase_S13_1w79D04 (D:5-459)
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Clan
:
Beta-lactamase
(210)
Family
:
Peptidase_S13
(9)
Actinomadura sp. (strain R39)
(8)
1a
Peptidase_S13-1w79D01
D:5-459
1b
Peptidase_S13-1w79D02
D:5-459
1c
Peptidase_S13-1w79D03
D:5-459
1d
Peptidase_S13-1w79D04
D:5-459
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Asymmetric Unit 1
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Asym.Unit (313 KB)
Header - Asym.Unit
Biol.Unit 1 (81 KB)
Header - Biol.Unit 1
Biol.Unit 2 (81 KB)
Header - Biol.Unit 2
Biol.Unit 3 (82 KB)
Header - Biol.Unit 3
Biol.Unit 4 (81 KB)
Header - Biol.Unit 4
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