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3KS5
Asym. Unit
Info
Asym.Unit (95 KB)
Biol.Unit 1 (44 KB)
Biol.Unit 2 (47 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF PUTATIVE GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE (17743486) FROM AGROBACTERIUM TUMEFACIENS STR. C58 (DUPONT) AT 2.05 A RESOLUTION
Authors
:
Joint Center For Structural Genomics (Jcsg)
Date
:
20 Nov 09 (Deposition) - 08 Dec 09 (Release) - 08 Dec 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.05
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Putative Glycerophosphoryl Diester Phosphodiesterase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Plasmid
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Glycerophosphoryl Diester Phosphodiesterase (17743486) From Agrobacterium Tumefaciens Str. C58 (Dupont) At 2. 05 A Resolution
To Be Published
(for further references see the
PDB file header
)
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Hetero Components
(4, 37)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
1c: ACETATE ION (ACTc)
1d: ACETATE ION (ACTd)
1e: ACETATE ION (ACTe)
1f: ACETATE ION (ACTf)
1g: ACETATE ION (ACTg)
2a: 1,2-ETHANEDIOL (EDOa)
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)
3a: FE (III) ION (FEa)
3b: FE (III) ION (FEb)
4a: SELENOMETHIONINE (MSEa)
4b: SELENOMETHIONINE (MSEb)
4c: SELENOMETHIONINE (MSEc)
4d: SELENOMETHIONINE (MSEd)
4e: SELENOMETHIONINE (MSEe)
4f: SELENOMETHIONINE (MSEf)
4g: SELENOMETHIONINE (MSEg)
4h: SELENOMETHIONINE (MSEh)
4i: SELENOMETHIONINE (MSEi)
4j: SELENOMETHIONINE (MSEj)
4k: SELENOMETHIONINE (MSEk)
4l: SELENOMETHIONINE (MSEl)
4m: SELENOMETHIONINE (MSEm)
4n: SELENOMETHIONINE (MSEn)
4o: SELENOMETHIONINE (MSEo)
4p: SELENOMETHIONINE (MSEp)
4q: SELENOMETHIONINE (MSEq)
4r: SELENOMETHIONINE (MSEr)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
7
Ligand/Ion
ACETATE ION
2
EDO
10
Ligand/Ion
1,2-ETHANEDIOL
3
FE
2
Ligand/Ion
FE (III) ION
4
MSE
18
Mod. Amino Acid
SELENOMETHIONINE
[
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]
Sites
(19, 19)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:34 , ASP A:36 , GLU A:104 , ACT A:251 , ACT A:252 , HOH A:268
BINDING SITE FOR RESIDUE FE A 250
02
AC2
SOFTWARE
HIS A:7 , ARG A:8 , HIS A:49 , GLU A:104 , LYS A:106 , FE A:250 , ACT A:252 , HOH A:288
BINDING SITE FOR RESIDUE ACT A 251
03
AC3
SOFTWARE
HIS A:7 , GLU A:34 , GLU A:104 , LEU A:158 , THR A:229 , FE A:250 , ACT A:251 , HOH A:316
BINDING SITE FOR RESIDUE ACT A 252
04
AC4
SOFTWARE
GLN A:165
BINDING SITE FOR RESIDUE ACT A 253
05
AC5
SOFTWARE
MSE A:196 , GLN A:200 , ASP A:205 , PHE A:206 , LYS A:226
BINDING SITE FOR RESIDUE ACT A 254
06
AC6
SOFTWARE
SER A:160 , PRO A:161 , SER A:162 , SER B:162 , GLN B:166
BINDING SITE FOR RESIDUE EDO A 255
07
AC7
SOFTWARE
ARG A:8 , ASP A:16 , HIS A:48 , HIS A:49 , ASP A:50 , THR A:56 , HOH A:286 , HOH A:301
BINDING SITE FOR RESIDUE EDO A 256
08
AC8
SOFTWARE
GLU A:174 , MSE B:1 , GLU B:31 , ARG B:240 , ARG B:244 , HOH B:276 , HOH B:374
BINDING SITE FOR RESIDUE EDO A 257
09
AC9
SOFTWARE
LEU A:167 , GLY A:168 , GLY A:170 , ALA A:171 , HOH A:315 , ALA B:142 , HOH B:414
BINDING SITE FOR RESIDUE EDO A 258
10
BC1
SOFTWARE
GLY A:0 , MSE A:1 , THR A:2 , GLY A:224 , HOH A:357
BINDING SITE FOR RESIDUE EDO A 259
11
BC2
SOFTWARE
GLU B:34 , ASP B:36 , GLU B:104 , ACT B:251 , ACT B:252 , HOH B:260
BINDING SITE FOR RESIDUE FE B 250
12
BC3
SOFTWARE
HIS B:7 , ARG B:8 , HIS B:49 , GLU B:104 , LYS B:106 , FE B:250 , ACT B:252 , HOH B:382
BINDING SITE FOR RESIDUE ACT B 251
13
BC4
SOFTWARE
HIS B:7 , GLU B:34 , GLU B:104 , LEU B:158 , TRP B:209 , THR B:229 , FE B:250 , ACT B:251 , HOH B:297
BINDING SITE FOR RESIDUE ACT B 252
14
BC5
SOFTWARE
LYS A:106 , PRO A:107 , PHE A:139 , HOH A:356 , GLN B:165 , GLN B:166
BINDING SITE FOR RESIDUE ACT B 253
15
BC6
SOFTWARE
ASP A:145 , HOH A:322 , LEU B:167 , GLY B:168 , GLY B:170 , ALA B:171 , HOH B:428
BINDING SITE FOR RESIDUE EDO B 254
16
BC7
SOFTWARE
ARG B:8 , ASP B:16 , HIS B:49 , ASP B:50 , THR B:56 , HOH B:271
BINDING SITE FOR RESIDUE EDO B 255
17
BC8
SOFTWARE
GLU A:174 , ALA B:178 , THR B:241 , ARG B:244
BINDING SITE FOR RESIDUE EDO B 256
18
BC9
SOFTWARE
PRO B:113 , ALA B:142 , GLU B:146 , HOH B:401
BINDING SITE FOR RESIDUE EDO B 257
19
CC1
SOFTWARE
PRO B:161 , ASP B:189
BINDING SITE FOR RESIDUE EDO B 258
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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End label:
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, 2)
Info
All SCOP Domains
1a: SCOP_d3ks5a_ (A:)
1b: SCOP_d3ks5b_ (B:)
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Protein Domains
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Organisms
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)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
PLC-like phosphodiesterases
(46)
Family
:
automated matches
(11)
Protein domain
:
automated matches
(11)
Agrobacterium tumefaciens [TaxId: 176299]
(2)
1a
d3ks5a_
A:
1b
d3ks5b_
B:
[
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Sorry, no Info available
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Pfam Domains
(0, 0)
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Sorry, no Info available
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Asymmetric Unit 1
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select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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set fontsize 20
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Asym.Unit (95 KB)
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Header - Biol.Unit 1
Biol.Unit 2 (47 KB)
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