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1TEZ
Asym. Unit
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
)
[
close entry info
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Hetero Components
(6, 18)
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
4
Ligand/Ion
CYTIDINE-5'-MONOPHOSPHATE
2
FAD
4
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
3
G
2
Ligand/Ion
GUANOSINE-5'-MONOPHOSPHATE
4
HDF
4
Ligand/Ion
8-HYDROXY-10-(D-RIBO-2,3,4,5-TETRAHYDROXYPENTYL)-5-DEAZAISOALLOXAZINE
5
MG
2
Ligand/Ion
MAGNESIUM ION
6
TCP
2
Mod. Nucleotide
5'-METHYLTHYMIDINE
[
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]
Sites
(16, 16)
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)
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
AC2
SOFTWARE
ASP A:399 , HOH A:9410 , HOH A:9411 , DC J:12 , HOH J:1610 , HOH J:1611
BINDING SITE FOR RESIDUE MG A 9002
03
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
04
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
05
AC5
SOFTWARE
ASN A:407 , GLN A:461 , G I:14
BINDING SITE FOR RESIDUE C I 15
06
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
07
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
08
AC8
SOFTWARE
ASN B:407 , GLN B:461 , G K:14
BINDING SITE FOR RESIDUE C K 15
09
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
10
BC1
SOFTWARE
ARG A:10 , PHE A:35 , CYS A:36 , LEU A:37 , ASP A:38 , ILE A:41 , LEU A:42 , MET A:47 , ARG A:51 , LEU A:55 , ASP A:101 , GLU A:103 , GLY A:106 , ARG A:109 , LYS A:248 , PHE A:249 , HOH A:9003 , HOH A:9102 , HOH A:9112
BINDING SITE FOR RESIDUE HDF A 5486
11
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
12
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
13
BC4
SOFTWARE
TYR C:228 , THR C:240 , SER C:241 , GLY C:242 , LEU C:243 , SER C:244 , LEU C:247 , TRP C:280 , GLU C:283 , ARG C:287 , TYR C:290 , TRP C:346 , ASN C:349 , ARG C:352 , LEU C:378 , ASP C:380 , GLY C:381 , ASP C:382 , ALA C:385 , ASN C:386 , GLY C:389 , TRP C:390 , HOH C:7496 , HOH C:7498 , HOH C:7506 , HOH C:7508 , HOH C:7509 , HOH C:7510 , HOH C:7836
BINDING SITE FOR RESIDUE FAD C 7485
14
BC5
SOFTWARE
ARG C:10 , PHE C:35 , CYS C:36 , LEU C:37 , ASP C:38 , ILE C:41 , LEU C:42 , MET C:47 , ARG C:51 , LEU C:55 , ASP C:101 , GLU C:103 , GLY C:106 , ARG C:109 , LYS C:248 , PHE C:249 , HOH C:7488 , HOH C:7589 , HOH C:7599
BINDING SITE FOR RESIDUE HDF C 7486
15
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
16
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
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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]
PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: PHR_CRY_ALPHA_BETA (A:3-132,B:3-132,C:3-132,D:3-132)
2: DNA_PHOTOLYASES_1_1 (A:329-341,B:329-341,C:329-341,D:32...)
;
View:
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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
4
A:3-132
B:3-132
C:3-132
D:3-132
2
DNA_PHOTOLYASES_1_1
PS00394
DNA photolyases class 1 signature 1.
PHR_SYNP6
329-341
4
A:329-341
B:329-341
C:329-341
D:329-341
[
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]
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
(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)
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Topologies
(
)
(
)
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(
)
(
)
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
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Organisms
(
)
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)
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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Asym.Unit (376 KB)
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