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Asym. Unit
Info
Asym.Unit (130 KB)
Biol.Unit 1 (123 KB)
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(1)
Title
:
HIGH RESOLUTION STRUCTURE OF THE CADMIUM-CONTAINING PHOSPHOTRIESTERASE FROM PSEUDOMONAS DIMINUTA
Authors
:
M. M. Benning, H. Shim, F. M. Raushel, H. M. Holden
Date
:
26 Jun 01 (Deposition) - 04 Jul 01 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.30
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Pte, Cadmium, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. M. Benning, H. Shim, F. M. Raushel, H. M. Holden
High Resolution X-Ray Structures Of Different Metal-Substituted Forms Of Phosphotriesterase From Pseudomonas Diminuta.
Biochemistry V. 40 2712 2001
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(5, 38)
Info
All Hetero Components
1a: CADMIUM ION (CDa)
1b: CADMIUM ION (CDb)
1c: CADMIUM ION (CDc)
1d: CADMIUM ION (CDd)
2a: 1,2-ETHANEDIOL (EDOa)
2aa: 1,2-ETHANEDIOL (EDOaa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
2g: 1,2-ETHANEDIOL (EDOg)
2h: 1,2-ETHANEDIOL (EDOh)
2i: 1,2-ETHANEDIOL (EDOi)
2j: 1,2-ETHANEDIOL (EDOj)
2k: 1,2-ETHANEDIOL (EDOk)
2l: 1,2-ETHANEDIOL (EDOl)
2m: 1,2-ETHANEDIOL (EDOm)
2n: 1,2-ETHANEDIOL (EDOn)
2o: 1,2-ETHANEDIOL (EDOo)
2p: 1,2-ETHANEDIOL (EDOp)
2q: 1,2-ETHANEDIOL (EDOq)
2r: 1,2-ETHANEDIOL (EDOr)
2s: 1,2-ETHANEDIOL (EDOs)
2t: 1,2-ETHANEDIOL (EDOt)
2u: 1,2-ETHANEDIOL (EDOu)
2v: 1,2-ETHANEDIOL (EDOv)
2w: 1,2-ETHANEDIOL (EDOw)
2x: 1,2-ETHANEDIOL (EDOx)
2y: 1,2-ETHANEDIOL (EDOy)
2z: 1,2-ETHANEDIOL (EDOz)
3a: LYSINE NZ-CARBOXYLIC ACID (KCXa)
3b: LYSINE NZ-CARBOXYLIC ACID (KCXb)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
5a: 2-PHENYL-ETHANOL (PELa)
5b: 2-PHENYL-ETHANOL (PELb)
5c: 2-PHENYL-ETHANOL (PELc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CD
4
Ligand/Ion
CADMIUM ION
2
EDO
27
Ligand/Ion
1,2-ETHANEDIOL
3
KCX
2
Mod. Amino Acid
LYSINE NZ-CARBOXYLIC ACID
4
NA
2
Ligand/Ion
SODIUM ION
5
PEL
3
Ligand/Ion
2-PHENYL-ETHANOL
[
close Hetero Component info
]
Sites
(36, 36)
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)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
EDO A:8 , HIS A:55 , HIS A:57 , KCX A:169 , ASP A:301 , HOH A:590
BINDING SITE FOR RESIDUE CD A 1
02
AC2
SOFTWARE
KCX A:169 , HIS A:201 , HIS A:230 , HOH A:590 , HOH A:646 , HOH A:699
BINDING SITE FOR RESIDUE CD A 2
03
AC3
SOFTWARE
EDO B:7 , HIS B:55 , HIS B:57 , KCX B:169 , ASP B:301 , HOH B:721
BINDING SITE FOR RESIDUE CD B 3
04
AC4
SOFTWARE
KCX B:169 , HIS B:201 , HIS B:230 , HOH B:606 , HOH B:681 , HOH B:721
BINDING SITE FOR RESIDUE CD B 4
05
AC5
SOFTWARE
ASN A:38 , ILE A:154 , HOH A:371 , HOH A:376 , HOH A:557 , HOH A:615
BINDING SITE FOR RESIDUE NA A 5
06
AC6
SOFTWARE
ASN B:38 , ILE B:154 , HOH B:391 , HOH B:559 , HOH B:566 , HOH B:593
BINDING SITE FOR RESIDUE NA B 6
07
AC7
SOFTWARE
CD B:3 , EDO B:20 , HIS B:57 , TRP B:131 , KCX B:169 , PHE B:306 , SER B:308 , EDO B:368 , HOH B:606 , HOH B:721
BINDING SITE FOR RESIDUE EDO B 7
08
AC8
SOFTWARE
CD A:1 , EDO A:22 , HIS A:57 , TRP A:131 , KCX A:169 , PHE A:306 , HOH A:648 , HOH A:699
BINDING SITE FOR RESIDUE EDO A 8
09
AC9
SOFTWARE
ARG A:91 , ARG B:189 , HOH B:481 , HOH B:567 , HOH B:700
BINDING SITE FOR RESIDUE EDO B 9
10
BC1
SOFTWARE
HOH A:469 , HOH A:568 , HOH A:577 , HOH A:602
BINDING SITE FOR RESIDUE EDO A 10
11
BC2
SOFTWARE
VAL A:84 , GLU A:115 , ALA A:119 , HOH A:430 , HOH A:595
BINDING SITE FOR RESIDUE EDO A 11
12
BC3
SOFTWARE
EDO A:13 , THR A:147 , ARG A:189 , HOH A:487 , HOH A:554 , HOH A:607 , ARG B:91
BINDING SITE FOR RESIDUE EDO A 12
13
BC4
SOFTWARE
EDO A:12 , HOH A:607 , ARG B:91 , ASP B:121
BINDING SITE FOR RESIDUE EDO A 13
14
BC5
SOFTWARE
EDO B:24 , ARG B:76 , LYS B:77 , GLU B:115 , HOH B:424 , HOH B:610
BINDING SITE FOR RESIDUE EDO B 14
15
BC6
SOFTWARE
GLY B:305 , PHE B:306 , MET B:314 , HOH B:540 , HOH B:723
BINDING SITE FOR RESIDUE EDO B 15
16
BC7
SOFTWARE
PRO B:256 , VAL B:320 , PHE B:327 , HOH B:575
BINDING SITE FOR RESIDUE EDO B 16
17
BC8
SOFTWARE
ASP A:133 , PRO A:135 , HOH A:712 , ASP B:133 , PRO B:134 , PRO B:135 , HOH B:370 , HOH B:372
BINDING SITE FOR RESIDUE EDO B 17
18
BC9
SOFTWARE
HOH A:390
BINDING SITE FOR RESIDUE EDO A 18
19
CC1
SOFTWARE
PRO A:256 , TRP A:277 , VAL A:320 , PHE A:327 , HOH A:591
BINDING SITE FOR RESIDUE EDO A 19
20
CC2
SOFTWARE
EDO B:7 , HIS B:257 , ASP B:301 , HOH B:721 , HOH B:742
BINDING SITE FOR RESIDUE EDO B 20
21
CC3
SOFTWARE
ARG A:41 , PRO A:43 , GLU B:338 , HOH B:580
BINDING SITE FOR RESIDUE EDO A 21
22
CC4
SOFTWARE
EDO A:8 , PHE A:306 , SER A:308 , HOH A:597
BINDING SITE FOR RESIDUE EDO A 22
23
CC5
SOFTWARE
SER A:224 , ARG A:225 , LEU A:249 , ARG A:356 , PHE A:357 , HOH A:609
BINDING SITE FOR RESIDUE EDO A 23
24
CC6
SOFTWARE
EDO B:14 , ALA B:80 , GLU B:81 , GLU B:115 , HOH B:648
BINDING SITE FOR RESIDUE EDO B 24
25
CC7
SOFTWARE
ALA A:266 , SER A:269 , ALA A:270
BINDING SITE FOR RESIDUE EDO A 25
26
CC8
SOFTWARE
HOH A:586 , HOH A:671 , TYR B:156 , HOH B:466 , HOH B:656
BINDING SITE FOR RESIDUE EDO B 26
27
CC9
SOFTWARE
PHE A:73 , GLY A:74 , ALA A:78 , HOH A:589 , HOH A:629
BINDING SITE FOR RESIDUE EDO A 27
28
DC1
SOFTWARE
LYS A:285 , ILE A:288 , ASP A:289 , VAL A:341 , PRO A:342 , HOH A:523
BINDING SITE FOR RESIDUE EDO A 28
29
DC2
SOFTWARE
GLY A:305 , PHE A:306 , MET A:314 , HOH A:422 , HOH A:526
BINDING SITE FOR RESIDUE EDO A 29
30
DC3
SOFTWARE
ARG A:152 , TYR A:156 , GLU B:71 , HOH B:377 , HOH B:658
BINDING SITE FOR RESIDUE EDO B 366
31
DC4
SOFTWARE
ILE A:333 , ARG A:337 , GLN A:343 , HOH A:394 , TYR B:156 , HOH B:469 , HOH B:674
BINDING SITE FOR RESIDUE EDO B 367
32
DC5
SOFTWARE
THR A:173 , HOH A:605
BINDING SITE FOR RESIDUE EDO A 366
33
DC6
SOFTWARE
EDO B:7 , SER B:308 , TYR B:309
BINDING SITE FOR RESIDUE EDO B 368
34
DC7
SOFTWARE
LYS B:77 , MET B:293 , GLY B:348 , ASN B:353
BINDING SITE FOR RESIDUE PEL B 369
35
DC8
SOFTWARE
LYS A:77 , MET A:293 , THR A:345 , GLY A:348 , ILE A:349 , ASN A:353
BINDING SITE FOR RESIDUE PEL A 367
36
DC9
SOFTWARE
ARG A:88 , ARG A:89 , HOH A:580 , LEU B:362 , ARG B:363
BINDING SITE FOR RESIDUE PEL A 368
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: PHOSPHOTRIESTERASE_2 (A:35-363,B:35-363)
2: PHOSPHOTRIESTERASE_1 (A:50-58,B:50-58)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PHOSPHOTRIESTERASE_2
PS51347
Phosphotriesterase family profile.
OPD_BREDI
35-363
2
A:35-363
B:35-363
2
PHOSPHOTRIESTERASE_1
PS01322
Phosphotriesterase family signature 1.
OPD_BREDI
50-58
2
A:50-58
B:50-58
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1jgma_ (A:)
1b: SCOP_d1jgmb_ (B:)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Metallo-dependent hydrolases
(273)
Family
:
Phosphotriesterase-like
(43)
Protein domain
:
Phosphotriesterase (parathion hydrolase, PTE)
(39)
Pseudomonas diminuta [TaxId: 293]
(19)
1a
d1jgma_
A:
1b
d1jgmb_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1jgmB00 (B:34-365)
1b: CATH_1jgmA00 (A:33-365)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Metal-dependent hydrolases
(190)
Brevundimonas diminuta. Organism_taxid: 293.
(7)
1a
1jgmB00
B:34-365
1b
1jgmA00
A:33-365
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_PTE_1jgmB01 (B:44-359)
1b: PFAM_PTE_1jgmB02 (B:44-359)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Amidohydrolase
(126)
Family
:
PTE
(19)
Brevundimonas diminuta (Pseudomonas diminuta)
(8)
1a
PTE-1jgmB01
B:44-359
1b
PTE-1jgmB02
B:44-359
[
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]
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