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2VTB
Asym. Unit
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
(5, 27)
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
8
Ligand/Ion
CHLORIDE ION
3
FAD
6
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
4
MHF
6
Ligand/Ion
5,10-METHENYL-6,7,8-TRIHYDROFOLIC ACID
5
TCP
6
Mod. Nucleotide
5'-METHYLTHYMIDINE
[
close Hetero Component info
]
Sites
(21, 21)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR A:272 , SER A:285 , THR A:286 , LYS A:287 , PHE A:288 , SER A:289 , LEU A:292 , GLU A:325 , ARG A:329 , PHE A:388 , ASN A:391 , ARG A:394 , GLN A:395 , LEU A:420 , ASP A:422 , TYR A:423 , ASP A:424 , SER A:427 , ASN A:428 , ASN A:431 , TRP A:432 , HOH A:2173 , HOH A:2174 , HOH A:2240 , HOH A:2269 , HOH A:2270 , DT G:2 , TCP G:3
BINDING SITE FOR RESIDUE FAD A 998
02
AC2
SOFTWARE
HIS A:83 , LYS A:89 , CYS A:146 , SER A:147 , GLU A:148 , GLU A:149 , ASN A:341 , PHE A:344 , HIS A:345 , GLU A:417 , TYR A:423 , PRO A:425 , TYR A:429 , HOH A:2271 , HOH A:2272 , PHE B:188 , ASP B:189 , ASP B:192 , LYS B:338
BINDING SITE FOR RESIDUE MHF A 999
03
AC3
SOFTWARE
ARG A:51 , ASP A:54 , ASP A:56 , HIS A:142 , ARG A:300 , HOH A:2190
BINDING SITE FOR RESIDUE CL A1501
04
AC4
SOFTWARE
TYR B:272 , SER B:285 , THR B:286 , LYS B:287 , PHE B:288 , SER B:289 , LEU B:292 , GLU B:325 , ARG B:329 , PHE B:332 , PHE B:388 , ASN B:391 , ARG B:394 , LEU B:420 , ASP B:422 , TYR B:423 , ASP B:424 , ASN B:428 , ASN B:431 , TRP B:432 , HOH B:2123 , HOH B:2124 , HOH B:2158 , HOH B:2168 , HOH B:2176 , DT H:2 , TCP H:3
BINDING SITE FOR RESIDUE FAD B 998
05
AC5
SOFTWARE
PHE A:188 , ASP A:189 , LYS A:338 , HOH A:2129 , HIS B:83 , LYS B:89 , CYS B:146 , SER B:147 , GLU B:148 , GLU B:149 , ASN B:341 , PHE B:344 , HIS B:345 , GLU B:417 , TYR B:423 , PRO B:425 , TYR B:429 , HOH B:2178
BINDING SITE FOR RESIDUE MHF B 999
06
AC6
SOFTWARE
ARG B:51 , ASP B:54 , ASP B:56 , HIS B:142 , ARG B:300
BINDING SITE FOR RESIDUE CL B1498
07
AC7
SOFTWARE
GLY B:281 , HOH B:2108 , HOH B:2175
BINDING SITE FOR RESIDUE CL B1499
08
AC8
SOFTWARE
ARG B:119 , ASP B:224 , ASP B:225
BINDING SITE FOR RESIDUE ACT B1500
09
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
10
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
11
BC2
SOFTWARE
ARG C:51 , ASP C:54 , ASP C:56 , HIS C:142 , ARG C:300
BINDING SITE FOR RESIDUE CL C1499
12
BC3
SOFTWARE
GLY C:281 , HOH C:2142 , HOH C:2243
BINDING SITE FOR RESIDUE CL C1500
13
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
14
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
15
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
16
BC7
SOFTWARE
TYR E:272 , SER E:285 , THR E:286 , LYS E:287 , PHE E:288 , SER E:289 , LEU E:292 , GLU E:325 , ARG E:329 , PHE E:332 , PHE E:388 , ASN E:391 , ARG E:394 , GLN E:395 , LEU E:420 , ASP E:422 , TYR E:423 , ASP E:424 , SER E:427 , ASN E:428 , ASN E:431 , TRP E:432 , HOH E:2146 , HOH E:2147 , HOH E:2197 , HOH E:2211 , HOH E:2230 , DT K:2 , TCP K:3
BINDING SITE FOR RESIDUE FAD E 998
17
BC8
SOFTWARE
LYS E:89 , CYS E:146 , SER E:147 , GLU E:148 , GLU E:149 , ASN E:341 , PHE E:344 , HIS E:345 , GLU E:417 , TYR E:423 , PRO E:425 , TYR E:429 , HOH E:2231 , HOH E:2233 , PHE F:188 , ASP F:189 , LYS F:338
BINDING SITE FOR RESIDUE MHF E 999
18
BC9
SOFTWARE
ARG E:51 , ASP E:54 , ASP E:56 , HIS E:142 , ARG E:300
BINDING SITE FOR RESIDUE CL E1499
19
CC1
SOFTWARE
TYR F:272 , SER F:285 , THR F:286 , LYS F:287 , PHE F:288 , SER F:289 , LEU F:292 , GLU F:325 , ARG F:329 , PHE F:388 , ASN F:391 , ARG F:394 , GLN F:395 , LEU F:420 , ASP F:422 , TYR F:423 , ASP F:424 , SER F:427 , ASN F:428 , ASN F:431 , TRP F:432 , HOH F:2077 , HOH F:2078 , HOH F:2106 , HOH F:2116 , DT L:2 , TCP L:3
BINDING SITE FOR RESIDUE FAD F 998
20
CC2
SOFTWARE
PHE E:188 , ASP E:189 , ASP E:192 , LYS E:338 , HOH E:2107 , HIS F:83 , LYS F:89 , CYS F:146 , SER F:147 , GLU F:148 , GLU F:149 , ASN F:341 , PHE F:344 , HIS F:345 , GLU F:417 , TYR F:423 , PRO F:425 , TYR F:429 , HOH F:2119
BINDING SITE FOR RESIDUE MHF F 999
21
CC3
SOFTWARE
HIS F:5 , GLY F:281 , HOH F:2068
BINDING SITE FOR RESIDUE CL F1498
[
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
(1, 6)
Info
All PROSITE Patterns/Profiles
1: PHR_CRY_ALPHA_BETA (A:40-177,B:40-177,C:40-177,D:40-17...)
;
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
6
A:40-177
B:40-177
C:40-177
D:40-177
E:40-177
F:40-177
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
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Label:
Sorry, no Info available
[
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
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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Asym.Unit (540 KB)
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