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1W8Y
Asym. Unit
Info
Asym.Unit (299 KB)
Biol.Unit 1 (77 KB)
Biol.Unit 2 (77 KB)
Biol.Unit 3 (77 KB)
Biol.Unit 4 (78 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE NITROCEFIN ACYL-DD-PEPTIDASE FROM ACTINOMADURA R39.
Authors
:
E. Sauvage, R. Herman, S. Petrella, C. Duez, J. M. Frere, P. Charlier
Date
:
01 Oct 04 (Deposition) - 28 Jun 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
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, Penicillin-Binding, Actinomadura, Peptidoglycan, Nitrocefin
(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
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Hetero Components
(3, 24)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
1c: MAGNESIUM ION (MGc)
1d: MAGNESIUM ION (MGd)
2a: (2R)-2-{(1R)-2-OXO-1-[(2-THIENYLAC... (NCFa)
2b: (2R)-2-{(1R)-2-OXO-1-[(2-THIENYLAC... (NCFb)
2c: (2R)-2-{(1R)-2-OXO-1-[(2-THIENYLAC... (NCFc)
2d: (2R)-2-{(1R)-2-OXO-1-[(2-THIENYLAC... (NCFd)
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
MG
4
Ligand/Ion
MAGNESIUM ION
2
NCF
4
Ligand/Ion
(2R)-2-{(1R)-2-OXO-1-[(2-THIENYLACETYL)AMINO]ETHYL}-5,6-DIHYDRO-2H-1,3-THIAZINE-4-CARBOXYLIC ACID
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
ASP A:281 , HIS A:282 , THR A:283 , HOH A:2186
BINDING SITE FOR RESIDUE SO4 A 501
02
AC2
SOFTWARE
ALA A:234 , ARG A:236
BINDING SITE FOR RESIDUE SO4 A 502
03
AC3
SOFTWARE
GLU A:132 , ARG A:133 , LEU A:134 , HOH A:2048
BINDING SITE FOR RESIDUE SO4 A 503
04
AC4
SOFTWARE
GLY A:159 , GLU A:160 , ARG A:161 , HOH A:2072 , HOH A:2188 , HOH A:2189 , HOH A:2190
BINDING SITE FOR RESIDUE SO4 A 504
05
AC5
SOFTWARE
ALA A:186 , GLU A:188 , HIS A:247 , GLU A:251
BINDING SITE FOR RESIDUE MG A 510
06
AC6
SOFTWARE
VAL A:406 , HIS A:462
BINDING SITE FOR RESIDUE MG A 511
07
AC7
SOFTWARE
ASP B:281 , HIS B:282 , THR B:283 , HOH B:2216 , HOH B:2217
BINDING SITE FOR RESIDUE SO4 B 501
08
AC8
SOFTWARE
ALA B:234 , ARG B:236 , HOH B:2219
BINDING SITE FOR RESIDUE SO4 B 502
09
AC9
SOFTWARE
SER B:131 , GLU B:132 , ARG B:133 , LEU B:134
BINDING SITE FOR RESIDUE SO4 B 503
10
BC1
SOFTWARE
GLY B:159 , GLU B:160 , ARG B:161 , HOH B:2222
BINDING SITE FOR RESIDUE SO4 B 504
11
BC2
SOFTWARE
ASP C:281 , HIS C:282 , THR C:283 , HOH C:2192 , HOH C:2193
BINDING SITE FOR RESIDUE SO4 C 501
12
BC3
SOFTWARE
ARG C:236 , HOH C:2133 , HOH C:2194
BINDING SITE FOR RESIDUE SO4 C 502
13
BC4
SOFTWARE
SER C:131 , ARG C:133 , LEU C:134 , HOH C:2063
BINDING SITE FOR RESIDUE SO4 C 503
14
BC5
SOFTWARE
HIS C:158 , GLY C:159 , GLU C:160 , ARG C:161 , HOH C:2197 , HOH C:2198
BINDING SITE FOR RESIDUE SO4 C 504
15
BC6
SOFTWARE
HIS D:282 , THR D:283 , HOH D:2132 , HOH D:2211 , HOH D:2212
BINDING SITE FOR RESIDUE SO4 D 501
16
BC7
SOFTWARE
ALA D:234 , ARG D:236 , HOH D:2213 , HOH D:2214
BINDING SITE FOR RESIDUE SO4 D 502
17
BC8
SOFTWARE
SER D:131 , GLU D:132 , ARG D:133 , LEU D:134 , HOH D:2215
BINDING SITE FOR RESIDUE SO4 D 503
18
BC9
SOFTWARE
HIS D:158 , GLY D:159 , GLU D:160 , ARG D:161 , HOH D:2217
BINDING SITE FOR RESIDUE SO4 D 504
19
CC1
SOFTWARE
GLU D:188 , HIS D:247 , GLU D:251
BINDING SITE FOR RESIDUE MG D 510
20
CC2
SOFTWARE
HIS D:462
BINDING SITE FOR RESIDUE MG D 511
21
CC3
SOFTWARE
ALA A:48 , SER A:49 , TYR A:147 , SER A:298 , ASN A:300 , LEU A:349 , THR A:411 , GLY A:412 , THR A:413 , MET A:414 , HOH A:2191 , GLU B:176 , HOH B:2109
BINDING SITE FOR RESIDUE NCF A 520
22
CC4
SOFTWARE
ALA B:48 , SER B:49 , TYR B:147 , SER B:298 , ASN B:300 , LEU B:349 , LYS B:410 , THR B:411 , GLY B:412 , THR B:413
BINDING SITE FOR RESIDUE NCF B 520
23
CC5
SOFTWARE
ALA C:48 , SER C:49 , TYR C:147 , SER C:298 , ASN C:300 , THR C:411 , GLY C:412 , THR C:413
BINDING SITE FOR RESIDUE NCF C 520
24
CC6
SOFTWARE
ALA D:48 , SER D:49 , ASP D:142 , TYR D:147 , SER D:298 , ASN D:300 , LEU D:349 , THR D:411 , GLY D:412 , THR D:413 , HOH D:2218
BINDING SITE FOR RESIDUE NCF D 520
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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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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_d1w8ya_ (A:)
1b: SCOP_d1w8yb_ (B:)
1c: SCOP_d1w8yc_ (C:)
1d: SCOP_d1w8yd_ (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
d1w8ya_
A:
1b
d1w8yb_
B:
1c
d1w8yc_
C:
1d
d1w8yd_
D:
[
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1w8yA01 (A:1-68,A:285-467)
1b: CATH_1w8yD01 (D:1-68,D:285-467)
1c: CATH_1w8yB01 (B:1-68,B:285-466)
1d: CATH_1w8yC01 (C:1-68,C:285-466)
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)
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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)
R39 (Actinomadura sp)
(1)
1a
1w8yA01
A:1-68,A:285-467
1b
1w8yD01
D:1-68,D:285-467
1c
1w8yB01
B:1-68,B:285-466
1d
1w8yC01
C:1-68,C:285-466
[
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Peptidase_S13_1w8yD01 (D:5-459)
1b: PFAM_Peptidase_S13_1w8yD02 (D:5-459)
1c: PFAM_Peptidase_S13_1w8yD03 (D:5-459)
1d: PFAM_Peptidase_S13_1w8yD04 (D:5-459)
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)
Clan
:
Beta-lactamase
(210)
Family
:
Peptidase_S13
(9)
Actinomadura sp. (strain R39)
(8)
1a
Peptidase_S13-1w8yD01
D:5-459
1b
Peptidase_S13-1w8yD02
D:5-459
1c
Peptidase_S13-1w8yD03
D:5-459
1d
Peptidase_S13-1w8yD04
D:5-459
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