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4DJ4
Asym. Unit
Info
Asym.Unit (103 KB)
Biol.Unit 1 (96 KB)
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(1)
Title
:
X-RAY STRUCTURE OF MUTANT N211D OF BIFUNCTIONAL NUCLEASE TBN1 FROM SOLANUM LYCOPERSICUM (TOMATO)
Authors
:
T. Koval, A. Stepankova, P. Lipovova, T. Podzimek, J. Matousek, J. Dusk T. Skalova, J. Hasek, J. Dohnalek
Date
:
01 Feb 12 (Deposition) - 07 Nov 12 (Release) - 20 Feb 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.35
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Mainly Alpha Helical, Trinuclear Metal Centre, Bi-Functional, Nuclease, 3'-Nucleotidase, Cytosol Membrane Associated, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Koval', P. Lipovova, T. Podzimek, J. Matousek, J. Duskova, T. Skalova, A. Stepankova, J. Hasek, J. Dohnalek
Plant Multifunctional Nuclease Tbn1 With Unexpected Phospholipase Activity: Structural Study And Reaction-Mechanism Analysis.
Acta Crystallogr. , Sect. D V. 69 213 2013
[
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Hetero Components
(6, 25)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
1c: BETA-D-MANNOSE (BMAc)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
3a: ALPHA-D-MANNOSE (MANa)
3b: ALPHA-D-MANNOSE (MANb)
3c: ALPHA-D-MANNOSE (MANc)
3d: ALPHA-D-MANNOSE (MANd)
3e: ALPHA-D-MANNOSE (MANe)
5a: N-ACETYL-D-GLUCOSAMINE (NAGa)
5b: N-ACETYL-D-GLUCOSAMINE (NAGb)
5c: N-ACETYL-D-GLUCOSAMINE (NAGc)
5d: N-ACETYL-D-GLUCOSAMINE (NAGd)
5e: N-ACETYL-D-GLUCOSAMINE (NAGe)
5f: N-ACETYL-D-GLUCOSAMINE (NAGf)
5g: N-ACETYL-D-GLUCOSAMINE (NAGg)
5h: N-ACETYL-D-GLUCOSAMINE (NAGh)
4a: SODIUM ION (NAa)
6a: ZINC ION (ZNa)
6b: ZINC ION (ZNb)
6c: ZINC ION (ZNc)
6d: ZINC ION (ZNd)
6e: ZINC ION (ZNe)
6f: ZINC ION (ZNf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
3
Ligand/Ion
BETA-D-MANNOSE
2
CL
2
Ligand/Ion
CHLORIDE ION
3
MAN
5
Ligand/Ion
ALPHA-D-MANNOSE
4
NA
1
Ligand/Ion
SODIUM ION
5
NAG
8
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
6
ZN
6
Ligand/Ion
ZINC ION
[
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Sites
(25, 25)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TRP A:26 , HIS A:31 , ASP A:151 , ZN A:402 , HOH A:701
BINDING SITE FOR RESIDUE ZN A 401
02
AC2
SOFTWARE
ASP A:70 , HIS A:85 , HIS A:147 , ASP A:151 , ZN A:401 , HOH A:701 , HOH A:703
BINDING SITE FOR RESIDUE ZN A 402
03
AC3
SOFTWARE
HIS A:157 , HIS A:181 , ASP A:185 , HOH A:702
BINDING SITE FOR RESIDUE ZN A 403
04
AC4
SOFTWARE
TRP A:80 , LEU A:84 , ASP A:110 , ASN A:119 , GLN A:123 , ARG A:135 , TYR A:136 , NAG A:502
BINDING SITE FOR RESIDUE NAG A 501
05
AC5
SOFTWARE
MET A:111 , NAG A:501
BINDING SITE FOR RESIDUE NAG A 502
06
AC6
SOFTWARE
TRP A:68 , TYR A:78 , ASN A:137 , GLU A:140 , NAG A:512 , HOH A:773 , LYS B:79
BINDING SITE FOR RESIDUE NAG A 511
07
AC7
SOFTWARE
PRO A:55 , TYR A:57 , NAG A:511 , BMA A:513 , CL A:601 , HOH A:714 , LYS B:79
BINDING SITE FOR RESIDUE NAG A 512
08
AC8
SOFTWARE
NAG A:512 , MAN A:514 , MAN A:515 , HOH A:738
BINDING SITE FOR RESIDUE BMA A 513
09
AC9
SOFTWARE
BMA A:513 , HOH A:749
BINDING SITE FOR RESIDUE MAN A 514
10
BC1
SOFTWARE
TYR A:57 , BMA A:513
BINDING SITE FOR RESIDUE MAN A 515
11
BC2
SOFTWARE
TRP A:68 , NAG A:512 , HOH A:728
BINDING SITE FOR RESIDUE CL A 601
12
BC3
SOFTWARE
TRP B:26 , HIS B:31 , ASP B:151 , ZN B:402 , HOH B:701
BINDING SITE FOR RESIDUE ZN B 401
13
BC4
SOFTWARE
ASP B:70 , HIS B:85 , HIS B:147 , ASP B:151 , ZN B:401 , HOH B:701 , HOH B:703
BINDING SITE FOR RESIDUE ZN B 402
14
BC5
SOFTWARE
ASP A:133 , HIS B:157 , HIS B:181 , ASP B:185 , HOH B:702
BINDING SITE FOR RESIDUE ZN B 403
15
BC6
SOFTWARE
TRP B:80 , LEU B:84 , ASP B:110 , MET B:111 , ALA B:116 , ASN B:119 , PHE B:120 , GLN B:123 , TYR B:136 , NAG B:502
BINDING SITE FOR RESIDUE NAG B 501
16
BC7
SOFTWARE
TRP B:80 , MET B:111 , NAG B:501 , BMA B:503
BINDING SITE FOR RESIDUE NAG B 502
17
BC8
SOFTWARE
NAG B:502 , MAN B:504 , HOH B:740
BINDING SITE FOR RESIDUE BMA B 503
18
BC9
SOFTWARE
BMA B:503 , HOH B:739 , HOH B:763
BINDING SITE FOR RESIDUE MAN B 504
19
CC1
SOFTWARE
LYS A:79 , SER A:82 , TRP B:68 , TYR B:78 , ASN B:137 , GLU B:140 , NAG B:512
BINDING SITE FOR RESIDUE NAG B 511
20
CC2
SOFTWARE
LYS A:79 , PRO B:55 , TYR B:57 , NAG B:511 , BMA B:513 , CL B:601 , HOH B:722
BINDING SITE FOR RESIDUE NAG B 512
21
CC3
SOFTWARE
NAG B:512 , MAN B:514 , MAN B:515
BINDING SITE FOR RESIDUE BMA B 513
22
CC4
SOFTWARE
ASP A:44 , HIS A:48 , BMA B:513 , HOH B:752
BINDING SITE FOR RESIDUE MAN B 514
23
CC5
SOFTWARE
BMA B:513
BINDING SITE FOR RESIDUE MAN B 515
24
CC6
SOFTWARE
TRP B:68 , NAG B:512
BINDING SITE FOR RESIDUE CL B 601
25
CC7
SOFTWARE
ARG B:100 , HIS B:103 , HOH B:736 , HOH B:741 , HOH B:743
BINDING SITE FOR RESIDUE NA B 602
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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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End label:
Sorry, no Info available
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Exons
(0, 0)
Info
All Exons
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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_d4dj4a_ (A:)
1b: SCOP_d4dj4b_ (B:)
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Protein Domains
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(
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Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Phospholipase C/P1 nuclease
(20)
Superfamily
:
Phospholipase C/P1 nuclease
(20)
Family
:
automated matches
(4)
Protein domain
:
automated matches
(4)
Solanum lycopersicum [TaxId: 4081]
(3)
1a
d4dj4a_
A:
1b
d4dj4b_
B:
[
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CATH Domains
(0, 0)
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all CATH domains
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Sorry, no Info available
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Pfam Domains
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Sorry, no Info available
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Atom Selection
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Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
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Asymmetric Unit 1
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select chains 'A' and 'C'
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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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Asym.Unit (103 KB)
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Header - Biol.Unit 1
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