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1TEZ
Biol. Unit 2
Info
Asym.Unit (376 KB)
Biol.Unit 1 (188 KB)
Biol.Unit 2 (192 KB)
Biol.Unit 3 (183 KB)
Biol.Unit 4 (262 KB)
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(1)
Title
:
COMPLEX BETWEEN DNA AND THE DNA PHOTOLYASE FROM ANACYSTIS NIDULANS
Authors
:
L. -O. Essen, T. Carell, A. Mees, T. Klar
Date
:
26 May 04 (Deposition) - 14 Dec 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,C,D,I,J,K,L,M,N,O,P
Biol. Unit 1: A,C,I,J,K (1x)
Biol. Unit 2: B,D,I,K,L,M,N (1x)
Biol. Unit 3: B,C,M,N,O,P (1x)
Biol. Unit 4: A,B,D,P (1x)
Keywords
:
Photolyase; Dna Repair; Light-Driven Electron Transfer, Lyase-Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Mees, T. Klar, P. Gnau, U. Hennecke, A. P. M. Eker, T. Carell, L. -O. Essen
Crystal Structure Of A Photolyase Bound To A Cpd-Like Dna Lesion After In Situ Repair
Science V. 306 1789 2004
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 6)
Info
All Hetero Components
1a: CYTIDINE-5'-MONOPHOSPHATE (Ca)
1b: CYTIDINE-5'-MONOPHOSPHATE (Cb)
1c: CYTIDINE-5'-MONOPHOSPHATE (Cc)
1d: CYTIDINE-5'-MONOPHOSPHATE (Cd)
2a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
2b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
2c: FLAVIN-ADENINE DINUCLEOTIDE (FADc)
2d: FLAVIN-ADENINE DINUCLEOTIDE (FADd)
3a: GUANOSINE-5'-MONOPHOSPHATE (Ga)
3b: GUANOSINE-5'-MONOPHOSPHATE (Gb)
4a: 8-HYDROXY-10-(D-RIBO-2,3,4,5-TETRA... (HDFa)
4b: 8-HYDROXY-10-(D-RIBO-2,3,4,5-TETRA... (HDFb)
4c: 8-HYDROXY-10-(D-RIBO-2,3,4,5-TETRA... (HDFc)
4d: 8-HYDROXY-10-(D-RIBO-2,3,4,5-TETRA... (HDFd)
5a: MAGNESIUM ION (MGa)
5b: MAGNESIUM ION (MGb)
6a: 5'-METHYLTHYMIDINE (TCPa)
6b: 5'-METHYLTHYMIDINE (TCPb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
C
-1
Ligand/Ion
CYTIDINE-5'-MONOPHOSPHATE
2
FAD
2
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
3
G
-1
Ligand/Ion
GUANOSINE-5'-MONOPHOSPHATE
4
HDF
2
Ligand/Ion
8-HYDROXY-10-(D-RIBO-2,3,4,5-TETRAHYDROXYPENTYL)-5-DEAZAISOALLOXAZINE
5
MG
-1
Ligand/Ion
MAGNESIUM ION
6
TCP
2
Mod. Nucleotide
5'-METHYLTHYMIDINE
[
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]
Sites
(12, 12)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC3 (SOFTWARE)
03: AC4 (SOFTWARE)
04: AC5 (SOFTWARE)
05: AC6 (SOFTWARE)
06: AC7 (SOFTWARE)
07: AC8 (SOFTWARE)
08: AC9 (SOFTWARE)
09: BC2 (SOFTWARE)
10: BC3 (SOFTWARE)
11: BC6 (SOFTWARE)
12: BC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP B:399 , HOH B:9305 , HOH B:9405 , DC L:12 , HOH L:1609
BINDING SITE FOR RESIDUE MG B 9001
02
AC3
SOFTWARE
ARG A:350 , GLN A:411 , TCP I:12 , G I:14 , HOH I:1450 , DG J:7 , DA J:8
BINDING SITE FOR RESIDUE C I 13
03
AC4
SOFTWARE
ILE A:405 , PHE A:406 , ASN A:407 , GLN A:411 , C I:13 , C I:15 , DC J:6 , DG J:7
BINDING SITE FOR RESIDUE G I 14
04
AC5
SOFTWARE
ASN A:407 , GLN A:461 , G I:14
BINDING SITE FOR RESIDUE C I 15
05
AC6
SOFTWARE
ARG B:350 , PHE B:406 , GLN B:411 , TCP K:12 , G K:14 , HOH K:1407 , DG L:7 , DA L:8
BINDING SITE FOR RESIDUE C K 13
06
AC7
SOFTWARE
ILE B:405 , PHE B:406 , ASN B:407 , GLN B:411 , LYS B:414 , C K:13 , C K:15 , DC L:6 , DG L:7
BINDING SITE FOR RESIDUE G K 14
07
AC8
SOFTWARE
ASN B:407 , GLN B:461 , G K:14
BINDING SITE FOR RESIDUE C K 15
08
AC9
SOFTWARE
TYR A:228 , THR A:240 , SER A:241 , GLY A:242 , LEU A:243 , SER A:244 , LEU A:247 , TRP A:280 , GLU A:283 , ARG A:287 , TYR A:290 , TRP A:346 , ASN A:349 , ARG A:352 , LEU A:378 , ASP A:380 , GLY A:381 , ASP A:382 , ALA A:385 , ASN A:386 , GLY A:389 , TRP A:390 , HOH A:9011 , HOH A:9013 , HOH A:9021 , HOH A:9022 , HOH A:9023 , HOH A:9024 , DT I:7 , TCP I:12
BINDING SITE FOR RESIDUE FAD A 5485
09
BC2
SOFTWARE
TYR B:228 , THR B:240 , SER B:241 , GLY B:242 , LEU B:243 , SER B:244 , LEU B:247 , TRP B:280 , GLU B:283 , ARG B:287 , TYR B:290 , TRP B:346 , ASN B:349 , ARG B:352 , LEU B:378 , ASP B:380 , GLY B:381 , ASP B:382 , ALA B:385 , ASN B:386 , GLY B:389 , TRP B:390 , HOH B:9010 , HOH B:9012 , HOH B:9020 , HOH B:9021 , HOH B:9022 , HOH B:9023 , DT K:7 , TCP K:12
BINDING SITE FOR RESIDUE FAD B 6485
10
BC3
SOFTWARE
ARG B:10 , PHE B:35 , CYS B:36 , LEU B:37 , ASP B:38 , ILE B:41 , LEU B:42 , MET B:47 , ARG B:51 , LEU B:55 , ASP B:101 , GLU B:103 , GLY B:106 , ARG B:109 , LYS B:248 , PHE B:249 , HOH B:9002 , HOH B:9102 , HOH B:9112
BINDING SITE FOR RESIDUE HDF B 6486
11
BC6
SOFTWARE
TYR D:228 , THR D:240 , SER D:241 , GLY D:242 , LEU D:243 , SER D:244 , LEU D:247 , TRP D:280 , GLU D:283 , ARG D:287 , TYR D:290 , TRP D:346 , MET D:347 , ASN D:349 , ARG D:352 , LEU D:378 , ASP D:380 , GLY D:381 , ASP D:382 , ALA D:385 , ASN D:386 , GLY D:389 , TRP D:390 , HOH D:8496 , HOH D:8498 , HOH D:8506 , HOH D:8508 , HOH D:8509 , HOH D:8510
BINDING SITE FOR RESIDUE FAD D 8485
12
BC7
SOFTWARE
ARG D:10 , PHE D:35 , CYS D:36 , LEU D:37 , ASP D:38 , ILE D:41 , LEU D:42 , MET D:47 , ARG D:51 , LEU D:55 , ASP D:101 , GLU D:103 , GLY D:106 , ARG D:109 , LYS D:248 , PHE D:249 , HOH D:8488 , HOH D:8588 , HOH D:8598
BINDING SITE FOR RESIDUE HDF D 8486
[
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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
(2, 4)
Info
All PROSITE Patterns/Profiles
1: PHR_CRY_ALPHA_BETA (B:3-132,D:3-132)
2: DNA_PHOTOLYASES_1_1 (B:329-341,D:329-341)
;
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.
PHR_SYNP6
3-132
2
-
B:3-132
-
D:3-132
2
DNA_PHOTOLYASES_1_1
PS00394
DNA photolyases class 1 signature 1.
PHR_SYNP6
329-341
2
-
B:329-341
-
D:329-341
[
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]
Exons
(0, 0)
Info
All Exons
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1teza1 (A:205-475)
1b: SCOP_d1tezb1 (B:205-475)
1c: SCOP_d1tezc1 (C:205-475)
1d: SCOP_d1tezd1 (D:205-475)
2a: SCOP_d1teza2 (A:2-204)
2b: SCOP_d1tezb2 (B:2-204)
2c: SCOP_d1tezc2 (C:2-204)
2d: SCOP_d1tezd2 (D:2-204)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Cryptochrome/photolyase FAD-binding domain
(26)
Superfamily
:
Cryptochrome/photolyase FAD-binding domain
(26)
Family
:
Cryptochrome/photolyase FAD-binding domain
(20)
Protein domain
:
C-terminal domain of DNA photolyase
(13)
Synechococcus elongatus [TaxId: 32046]
(7)
1a
d1teza1
A:205-475
1b
d1tezb1
B:205-475
1c
d1tezc1
C:205-475
1d
d1tezd1
D:205-475
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Cryptochrome/photolyase, N-terminal domain
(27)
Superfamily
:
Cryptochrome/photolyase, N-terminal domain
(27)
Family
:
Cryptochrome/photolyase, N-terminal domain
(17)
Protein domain
:
DNA photolyase
(13)
Synechococcus elongatus [TaxId: 32046]
(7)
2a
d1teza2
A:2-204
2b
d1tezb2
B:2-204
2c
d1tezc2
C:2-204
2d
d1tezd2
D:2-204
[
close SCOP info
]
CATH Domains
(3, 12)
Info
all CATH domains
1a: CATH_1tezA01 (A:2-129)
1b: CATH_1tezB01 (B:2-129)
1c: CATH_1tezC01 (C:2-129)
1d: CATH_1tezD01 (D:2-129)
2a: CATH_1tezA02 (A:130-164,A:210-297)
2b: CATH_1tezB02 (B:130-164,B:210-297)
2c: CATH_1tezC02 (C:130-164,C:210-297)
2d: CATH_1tezD02 (D:130-164,D:210-297)
3a: CATH_1tezA03 (A:298-473)
3b: CATH_1tezB03 (B:298-473)
3c: CATH_1tezC03 (C:298-473)
3d: CATH_1tezD03 (D:298-473)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1
(328)
[unclassified]
(27)
1a
1tezA01
A:2-129
1b
1tezB01
B:2-129
1c
1tezC01
C:2-129
1d
1tezD01
D:2-129
Class
:
Mainly Alpha
(13335)
Architecture
:
Alpha Horseshoe
(399)
Topology
:
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
(320)
Homologous Superfamily
:
[code=1.25.40.80, no name defined]
(16)
[unclassified]
(1)
2a
1tezA02
A:130-164,A:210-297
2b
1tezB02
B:130-164,B:210-297
2c
1tezC02
C:130-164,C:210-297
2d
1tezD02
D:130-164,D:210-297
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3
(16)
Homologous Superfamily
:
DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3
(16)
[unclassified]
(1)
3a
1tezA03
A:298-473
3b
1tezB03
B:298-473
3c
1tezC03
C:298-473
3d
1tezD03
D:298-473
[
close CATH info
]
Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_DNA_photolyase_1tezD01 (D:5-170)
1b: PFAM_DNA_photolyase_1tezD02 (D:5-170)
1c: PFAM_DNA_photolyase_1tezD03 (D:5-170)
1d: PFAM_DNA_photolyase_1tezD04 (D:5-170)
2a: PFAM_FAD_binding_7_1tezD05 (D:208-472)
2b: PFAM_FAD_binding_7_1tezD06 (D:208-472)
2c: PFAM_FAD_binding_7_1tezD07 (D:208-472)
2d: PFAM_FAD_binding_7_1tezD08 (D:208-472)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
HUP
(230)
Family
:
DNA_photolyase
(11)
Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1) (Anacystis nidulans)
(5)
1a
DNA_photolyase-1tezD01
D:5-170
1b
DNA_photolyase-1tezD02
D:5-170
1c
DNA_photolyase-1tezD03
D:5-170
1d
DNA_photolyase-1tezD04
D:5-170
Clan
:
no clan defined [family: FAD_binding_7]
(11)
Family
:
FAD_binding_7
(11)
Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1) (Anacystis nidulans)
(5)
2a
FAD_binding_7-1tezD05
D:208-472
2b
FAD_binding_7-1tezD06
D:208-472
2c
FAD_binding_7-1tezD07
D:208-472
2d
FAD_binding_7-1tezD08
D:208-472
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