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1NP7
Biol. Unit 1
Info
Asym.Unit (174 KB)
Biol.Unit 1 (87 KB)
Biol.Unit 2 (86 KB)
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(1)
Title
:
CRYSTAL STRUCTURE ANALYSIS OF SYNECHOCYSTIS SP. PCC6803 CRYPTOCHROME
Authors
:
R. Brudler, K. Hitomi, H. Daiyasu, H. Toh, K. Kucho, M. Ishiura, M. Kaneh V. A. Roberts, T. Todo, J. A. Tainer, E. D. Getzoff
Date
:
17 Jan 03 (Deposition) - 28 Jan 03 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Protein With Fad Cofactor, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
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)
Reference
:
R. Brudler, K. Hitomi, H. Daiyasu, H. Toh, K. Kucho, M. Ishiura, M. Kanehisa, V. A. Roberts, T. Todo, J. A. Tainer, E. D. Getzoff
Identification Of A New Cryptochrome Class: Structure, Function, And Evolution
Mol. Cell V. 11 59 2003
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Hetero Components
(2, 3)
Info
All Hetero Components
1a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
1b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FAD
1
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
2
SO4
2
Ligand/Ion
SULFATE ION
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Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC3 (SOFTWARE)
3: AC4 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU A:322 , ASP A:323 , GLN A:324 , VAL A:325 , HOH A:1305 , HOH A:1342
BINDING SITE FOR RESIDUE SO4 A 1401
2
AC3
SOFTWARE
ARG A:310 , ARG A:374 , HOH A:1348 , SER B:450 , ALA B:451
BINDING SITE FOR RESIDUE SO4 A 1403
3
AC4
SOFTWARE
TYR A:236 , SER A:249 , SER A:250 , LYS A:251 , PHE A:252 , SER A:253 , LEU A:256 , GLU A:289 , ARG A:293 , PHE A:296 , PHE A:352 , ASN A:355 , ARG A:358 , GLN A:359 , ALA A:362 , PHE A:380 , LEU A:384 , ASP A:386 , TYR A:387 , ASP A:388 , SER A:391 , ASN A:392 , ASN A:395 , TRP A:396 , HOH A:1016 , HOH A:1030 , HOH A:1037 , HOH A:1237 , HOH A:1238
BINDING SITE FOR RESIDUE FAD A 500
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: PHR_CRY_ALPHA_BETA (A:6-140)
2: DNA_PHOTOLYASES_1_1 (A:335-347)
;
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PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PHR_CRY_ALPHA_BETA
PS51645
Photolyase/cryptochrome alpha/beta domain profile.
CRYD_SYNY3
6-140
1
A:6-140
-
2
DNA_PHOTOLYASES_1_1
PS00394
DNA photolyases class 1 signature 1.
CRYD_SYNY3
335-347
1
A:335-347
-
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Exons
(0, 0)
Info
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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
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1np7a1 (A:205-483)
1b: SCOP_d1np7b1 (B:205-483)
2a: SCOP_d1np7a2 (A:1-204)
2b: SCOP_d1np7b2 (B:1-204)
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)
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)
(
)
Families
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)
(
)
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
:
Cryptochrome C-terminal domain
(4)
Synechocystis sp. PCC 6803 [TaxId: 1148]
(1)
1a
d1np7a1
A:205-483
1b
d1np7b1
B:205-483
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
:
Cryptochrome
(4)
Synechocystis sp. PCC 6803 [TaxId: 1148]
(1)
2a
d1np7a2
A:1-204
2b
d1np7b2
B:1-204
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CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_1np7B01 (B:1-137)
1b: CATH_1np7A01 (A:6-137)
2a: CATH_1np7A02 (A:141-169,A:213-302)
2b: CATH_1np7B02 (B:138-308)
3a: CATH_1np7B03 (B:309-483)
3b: CATH_1np7A03 (A:303-482)
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)
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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)
Pcc 6803 (Synechocystis sp)
(1)
1a
1np7B01
B:1-137
1b
1np7A01
A:6-137
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)
Pcc 6803 (Synechocystis sp)
(1)
2a
1np7A02
A:141-169,A:213-302
2b
1np7B02
B:138-308
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)
Pcc 6803 (Synechocystis sp)
(1)
3a
1np7B03
B:309-483
3b
1np7A03
A:303-482
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_DNA_photolyase_1np7B01 (B:8-183)
1b: PFAM_DNA_photolyase_1np7B02 (B:8-183)
2a: PFAM_FAD_binding_7_1np7B03 (B:214-483)
2b: PFAM_FAD_binding_7_1np7B04 (B:214-483)
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Families
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)
Organisms
(
)
(
)
Clan
:
HUP
(230)
Family
:
DNA_photolyase
(11)
Synechocystis sp. (strain ATCC 27184 / PCC 6803 / N-1)
(1)
1a
DNA_photolyase-1np7B01
B:8-183
1b
DNA_photolyase-1np7B02
B:8-183
Clan
:
no clan defined [family: FAD_binding_7]
(11)
Family
:
FAD_binding_7
(11)
Synechocystis sp. (strain ATCC 27184 / PCC 6803 / N-1)
(1)
2a
FAD_binding_7-1np7B03
B:214-483
2b
FAD_binding_7-1np7B04
B:214-483
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Chain A
Asymmetric Unit 1
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select chains 'A' and 'C'
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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