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2VTB
Biol. Unit 2
Info
Asym.Unit (540 KB)
Biol.Unit 1 (182 KB)
Biol.Unit 2 (181 KB)
Biol.Unit 3 (177 KB)
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(1)
Title
:
STRUCTURE OF CRYPTOCHROME 3 - DNA COMPLEX
Authors
:
R. Pokorny, T. Klar, U. Hennecke, T. Carell, A. Batschauer, L. -O. Esse
Date
:
13 May 08 (Deposition) - 02 Jun 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.01
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,G,H (1x)
Biol. Unit 2: C,D,I,J (1x)
Biol. Unit 3: E,F,K,L (1x)
Keywords
:
Lyase-Dna Complex, Lyase Dna Complex, Flavin Adenine Dinucleotide, Dna, Dna-Binding, Cryptochrome, Flavoprotein, Mitochondrion, Fad, Photolyase, Chromophore, Chloroplast, Transit Peptide, Single-Stranded Dna, Cyclobutane-Pyrimidine Dimer
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Pokorny, T. Klar, U. Hennecke, T. Carell, A. Batschauer, L. -O. Esse
Recognition And Repair Of Uv Lesions In Loop Structures Of Duplex Dna By Dash-Type Cryptochrome.
Proc. Natl. Acad. Sci. Usa V. 105 21023 2008
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 6)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
2e: CHLORIDE ION (CLe)
2f: CHLORIDE ION (CLf)
2g: CHLORIDE ION (CLg)
2h: CHLORIDE ION (CLh)
3a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
3b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
3c: FLAVIN-ADENINE DINUCLEOTIDE (FADc)
3d: FLAVIN-ADENINE DINUCLEOTIDE (FADd)
3e: FLAVIN-ADENINE DINUCLEOTIDE (FADe)
3f: FLAVIN-ADENINE DINUCLEOTIDE (FADf)
4a: 5,10-METHENYL-6,7,8-TRIHYDROFOLIC ... (MHFa)
4b: 5,10-METHENYL-6,7,8-TRIHYDROFOLIC ... (MHFb)
4c: 5,10-METHENYL-6,7,8-TRIHYDROFOLIC ... (MHFc)
4d: 5,10-METHENYL-6,7,8-TRIHYDROFOLIC ... (MHFd)
4e: 5,10-METHENYL-6,7,8-TRIHYDROFOLIC ... (MHFe)
4f: 5,10-METHENYL-6,7,8-TRIHYDROFOLIC ... (MHFf)
5a: 5'-METHYLTHYMIDINE (TCPa)
5b: 5'-METHYLTHYMIDINE (TCPb)
5c: 5'-METHYLTHYMIDINE (TCPc)
5d: 5'-METHYLTHYMIDINE (TCPd)
5e: 5'-METHYLTHYMIDINE (TCPe)
5f: 5'-METHYLTHYMIDINE (TCPf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
-1
Ligand/Ion
ACETATE ION
2
CL
-1
Ligand/Ion
CHLORIDE ION
3
FAD
2
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
4
MHF
2
Ligand/Ion
5,10-METHENYL-6,7,8-TRIHYDROFOLIC ACID
5
TCP
2
Mod. Nucleotide
5'-METHYLTHYMIDINE
[
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]
Sites
(7, 7)
Info
All Sites
1: AC9 (SOFTWARE)
2: BC1 (SOFTWARE)
3: BC2 (SOFTWARE)
4: BC3 (SOFTWARE)
5: BC4 (SOFTWARE)
6: BC5 (SOFTWARE)
7: BC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC9
SOFTWARE
TYR C:272 , SER C:285 , THR C:286 , LYS C:287 , PHE C:288 , SER C:289 , LEU C:292 , GLU C:325 , ARG C:329 , PHE C:332 , PHE C:388 , ASN C:391 , ARG C:394 , GLN C:395 , LEU C:420 , ASP C:422 , TYR C:423 , ASP C:424 , ASN C:428 , ASN C:431 , TRP C:432 , HOH C:2159 , HOH C:2161 , HOH C:2209 , HOH C:2223 , HOH C:2252 , DT I:2 , TCP I:3
BINDING SITE FOR RESIDUE FAD C 998
2
BC1
SOFTWARE
LYS C:89 , CYS C:146 , SER C:147 , GLU C:148 , GLU C:149 , ASN C:341 , PHE C:344 , HIS C:345 , GLU C:417 , TYR C:423 , PRO C:425 , TYR C:429 , HOH C:2253 , HOH C:2255 , HOH C:2256 , HOH C:2257 , PHE D:188 , ASP D:189 , LYS D:338
BINDING SITE FOR RESIDUE MHF C 999
3
BC2
SOFTWARE
ARG C:51 , ASP C:54 , ASP C:56 , HIS C:142 , ARG C:300
BINDING SITE FOR RESIDUE CL C1499
4
BC3
SOFTWARE
GLY C:281 , HOH C:2142 , HOH C:2243
BINDING SITE FOR RESIDUE CL C1500
5
BC4
SOFTWARE
TYR D:272 , SER D:285 , THR D:286 , LYS D:287 , PHE D:288 , SER D:289 , LEU D:292 , GLU D:325 , ARG D:329 , PHE D:332 , PHE D:388 , ASN D:391 , ARG D:394 , GLN D:395 , LEU D:420 , ASP D:422 , TYR D:423 , ASP D:424 , SER D:427 , ASN D:428 , ASN D:431 , TRP D:432 , HOH D:2143 , HOH D:2144 , HOH D:2190 , HOH D:2200 , HOH D:2205 , DT J:2 , TCP J:3
BINDING SITE FOR RESIDUE FAD D 998
6
BC5
SOFTWARE
PHE C:188 , ASP C:189 , ASP C:192 , LYS C:338 , LYS D:89 , CYS D:146 , SER D:147 , GLU D:148 , GLU D:149 , ASN D:341 , PHE D:344 , HIS D:345 , GLU D:417 , TYR D:423 , PRO D:425 , TYR D:429 , HOH D:2206 , HOH D:2208 , HOH D:2209
BINDING SITE FOR RESIDUE MHF D 999
7
BC6
SOFTWARE
ARG D:51 , ASP D:54 , ASP D:56 , HIS D:142 , ARG D:300 , HOH D:2160
BINDING SITE FOR RESIDUE CL D1498
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: PHR_CRY_ALPHA_BETA (C:40-177,D:40-177)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PHR_CRY_ALPHA_BETA
PS51645
Photolyase/cryptochrome alpha/beta domain profile.
CRYD_ARATH
84-221
2
-
-
C:40-177
D:40-177
-
-
[
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
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Sorry, no Info available
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
[
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Pfam Domains
(2, 12)
Info
all PFAM domains
1a: PFAM_DNA_photolyase_2vtbF01 (F:42-219)
1b: PFAM_DNA_photolyase_2vtbF02 (F:42-219)
1c: PFAM_DNA_photolyase_2vtbF03 (F:42-219)
1d: PFAM_DNA_photolyase_2vtbF04 (F:42-219)
1e: PFAM_DNA_photolyase_2vtbF05 (F:42-219)
1f: PFAM_DNA_photolyase_2vtbF06 (F:42-219)
2a: PFAM_FAD_binding_7_2vtbF07 (F:250-492)
2b: PFAM_FAD_binding_7_2vtbF08 (F:250-492)
2c: PFAM_FAD_binding_7_2vtbF09 (F:250-492)
2d: PFAM_FAD_binding_7_2vtbF10 (F:250-492)
2e: PFAM_FAD_binding_7_2vtbF11 (F:250-492)
2f: PFAM_FAD_binding_7_2vtbF12 (F:250-492)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
HUP
(230)
Family
:
DNA_photolyase
(11)
Arabidopsis thaliana (Mouse-ear cress)
(2)
1a
DNA_photolyase-2vtbF01
F:42-219
1b
DNA_photolyase-2vtbF02
F:42-219
1c
DNA_photolyase-2vtbF03
F:42-219
1d
DNA_photolyase-2vtbF04
F:42-219
1e
DNA_photolyase-2vtbF05
F:42-219
1f
DNA_photolyase-2vtbF06
F:42-219
Clan
:
no clan defined [family: FAD_binding_7]
(11)
Family
:
FAD_binding_7
(11)
Arabidopsis thaliana (Mouse-ear cress)
(2)
2a
FAD_binding_7-2vtbF07
F:250-492
2b
FAD_binding_7-2vtbF08
F:250-492
2c
FAD_binding_7-2vtbF09
F:250-492
2d
FAD_binding_7-2vtbF10
F:250-492
2e
FAD_binding_7-2vtbF11
F:250-492
2f
FAD_binding_7-2vtbF12
F:250-492
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Asymmetric Unit 1
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Asym.Unit (540 KB)
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Header - Biol.Unit 3
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