1NP7 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

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)] )

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
PubMed-ID: 12535521 | Reference-DOI: 10.1016/S1097-2765(03)00008-X

Molecule 1 - DNA PHOTOLYASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX 4T-2, PCC6803
	Expression System Strain	:	JM109
	Expression System Taxid	:	562
	Expression System Vector	:	PLASMID
	Organism Scientific	:	SYNECHOCYSTIS SP.
	Organism Taxid	:	1148
	Strain	:	PCC 6803

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 5)

No.	Name	Count	Type	Full Name
1	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (5, 5)

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	AC2	SOFTWARE	ARG B:356 , PHE B:412 , GLN B:417 , TYR B:421	BINDING SITE FOR RESIDUE SO4 B 1402
3	AC3	SOFTWARE	ARG A:310 , ARG A:374 , HOH A:1348 , SER B:450 , ALA B:451	BINDING SITE FOR RESIDUE SO4 A 1403
4	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
5	AC5	SOFTWARE	TYR B:236 , SER B:249 , SER B:250 , LYS B:251 , PHE B:252 , SER B:253 , LEU B:256 , GLU B:289 , ARG B:293 , PHE B:296 , PHE B:352 , ASN B:355 , ARG B:358 , GLN B:359 , ALA B:362 , PHE B:380 , LEU B:384 , ASP B:386 , TYR B:387 , ASP B:388 , SER B:391 , ASN B:392 , ASN B:395 , TRP B:396 , HOH B:1010 , HOH B:1022 , HOH B:1112 , HOH B:1279 , HOH B:1326	BINDING SITE FOR RESIDUE FAD B 501

(no "SS Bond" information available for 1NP7)

(no "Cis Peptide Bond" information available for 1NP7)

(no "SAP(SNP)/Variant" information available for 1NP7)

Asymmetric Unit (2, 4)

	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	2	A:6-140 B:6-140
2	DNA_PHOTOLYASES_1_1	PS00394	DNA photolyases class 1 signature 1.	CRYD_SYNY3	335-347	2	A:335-347 B:335-347

Biological Unit 1 (2, 2)

	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 -

Biological Unit 2 (2, 2)

	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	- B:6-140
2	DNA_PHOTOLYASES_1_1	PS00394	DNA photolyases class 1 signature 1.	CRYD_SYNY3	335-347	1	- B:335-347

(no "Exon" information available for 1NP7)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:483
 aligned with CRYD_SYNY3 | P77967 from UniProtKB/Swiss-Prot  Length:489

    Alignment length:483
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480   
           CRYD_SYNY3     1 MKHVPPTVLVWFRNDLRLHDHEPLHRALKSGLAITAVYCYDPRQFAQTHQGFAKTGPWRSNFLQQSVQNLAESLQKVGNKLLVTTGLPEQVIPQIAKQINAKTIYYHREVTQEELDVERNLVKQLTILGIEAKGYWGSTLCHPEDLPFSIQDLPDLFTKFRKDIEKKKISIRPCFFAPSQLLPSPNIKLELTAPPPEFFPQINFDHRSVLAFQGGETAGLARLQDYFWHGDRLKDYKETRNGMVGADYSSKFSPWLALGCLSPRFIYQEVKRYEQERVSNDSTHWLIFELLWRDFFRFVAQKYGNKLFNRGGLLNKNFPWQEDQVRFELWRSGQTGYPLVDANMRELNLTGFMSNRGRQNVASFLCKNLGIDWRWGAEWFESCLIDYDVCSNWGNWNYTAGIGNDARDFRYFNIPKQSQQYDPQGTYLRHWLPELKNLPGDKIHQPWLLSATEQKQWGVQLGVDYPRPCVNFHQSVEARRKIE 483
               SCOP domains d1np7a2 A:1-204 Cryptochrome                                                                                                                                                                                d1np7a1 A:205-483 Cryptochrome C-terminal domain                                                                                                                                                                                                                                        SCOP domains
               CATH domains -----1np7A01 A:6-137 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                               ---1np7A02 A:141-169,A:213-302  -------------------------------------------1np7A02 A:141-169,A:213-302  [code=1.25.40.80, no name defined]                           1np7A03 A:303-482 DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3                                                                                                      - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee........hhhhhhhhhh..eeeeeeeehhhhhh.........hhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhhhhhhhhh.eeeee......hhhhh..hhhhh..hhhhhhhhhhh............................hhhhh...............hhhhhhhhhhhhhh...hhhhhhhhh...........hhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhh............hhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.............hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----PHR_CRY_ALPHA_BETA  PDB: A:6-140 UniProt: 6-140                                                                                        --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_PHOTOLYAS---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1np7 A   1 MKHVPPTVLVWFRNDLRLHDHEPLHRALKSGLAITAVYCYDPRQFAQTHQGFAKTGPWRSNFLQQSVQNLAESLQKVGNKLLVTTGLPEQVIPQIAKQINAKTIYYHREVTQEELDVERNLVKQLTILGIEAKGYWGSTLCHPEDLPFSIQDLPDLFTKFRKDIEKKKISIRPCFFAPSQLLPSPNIKLELTAPPPEFFPQINFDHRSVLAFQGGETAGLARLQDYFWHGDRLKDYKETRNGMVGADYSSKFSPWLALGCLSPRFIYQEVKRYEQERVSNDSTHWLIFELLWRDFFRFVAQKYGNKLFNRGGLLNKNFPWQEDQVRFELWRSGQTGYPLVDANMRELNLTGFMSNRGRQNVASFLCKNLGIDWRWGAEWFESCLIDYDVCSNWGNWNYTAGIGNDARDFRYFNIPKQSQQYDPQGTYLRHWLPELKNLPGDKIHQPWLLSATEQKQWGVQLGVDYPRPCVNFHQSVEARRKIE 483
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480

Chain B from PDB  Type:PROTEIN  Length:483
 aligned with CRYD_SYNY3 | P77967 from UniProtKB/Swiss-Prot  Length:489

    Alignment length:483
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480   
           CRYD_SYNY3     1 MKHVPPTVLVWFRNDLRLHDHEPLHRALKSGLAITAVYCYDPRQFAQTHQGFAKTGPWRSNFLQQSVQNLAESLQKVGNKLLVTTGLPEQVIPQIAKQINAKTIYYHREVTQEELDVERNLVKQLTILGIEAKGYWGSTLCHPEDLPFSIQDLPDLFTKFRKDIEKKKISIRPCFFAPSQLLPSPNIKLELTAPPPEFFPQINFDHRSVLAFQGGETAGLARLQDYFWHGDRLKDYKETRNGMVGADYSSKFSPWLALGCLSPRFIYQEVKRYEQERVSNDSTHWLIFELLWRDFFRFVAQKYGNKLFNRGGLLNKNFPWQEDQVRFELWRSGQTGYPLVDANMRELNLTGFMSNRGRQNVASFLCKNLGIDWRWGAEWFESCLIDYDVCSNWGNWNYTAGIGNDARDFRYFNIPKQSQQYDPQGTYLRHWLPELKNLPGDKIHQPWLLSATEQKQWGVQLGVDYPRPCVNFHQSVEARRKIE 483
               SCOP domains d1np7b2 B:1-204 Cryptochrome                                                                                                                                                                                d1np7b1 B:205-483 Cryptochrome C-terminal domain                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1np7B01 B:1-137 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                    1np7B02 B:138-308  [code=1.25.40.80, no name defined]                                                                                                                      1np7B03 B:309-483 DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3                                                                                                  CATH domains
           Pfam domains (1) -------DNA_photolyase-1np7B01 B:8-183                                                                                                                                                  ------------------------------FAD_binding_7-1np7B03 B:214-483                                                                                                                                                                                                                                                Pfam domains (1)
           Pfam domains (2) -------DNA_photolyase-1np7B02 B:8-183                                                                                                                                                  ------------------------------FAD_binding_7-1np7B04 B:214-483                                                                                                                                                                                                                                                Pfam domains (2)
         Sec.struct. author ......eeeeee........hhhhhhhhh....eeeeeeehhhhhh.........hhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhhhhhhhh..eeeee......hhhhh..hhhhh..hhhhhhhhhhh............................hhhhh...............hhhhhhhhhhhhhh...hhhhhhhhh...........hhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhh............hhhhhhhhhh..hhhhhhhhhhhh........hhhhhhhhhhhhh.............hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----PHR_CRY_ALPHA_BETA  PDB: B:6-140 UniProt: 6-140                                                                                        --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_PHOTOLYAS---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1np7 B   1 MKHVPPTVLVWFRNDLRLHDHEPLHRALKSGLAITAVYCYDPRQFAQTHQGFAKTGPWRSNFLQQSVQNLAESLQKVGNKLLVTTGLPEQVIPQIAKQINAKTIYYHREVTQEELDVERNLVKQLTILGIEAKGYWGSTLCHPEDLPFSIQDLPDLFTKFRKDIEKKKISIRPCFFAPSQLLPSPNIKLELTAPPPEFFPQINFDHRSVLAFQGGETAGLARLQDYFWHGDRLKDYKETRNGMVGADYSSKFSPWLALGCLSPRFIYQEVKRYEQERVSNDSTHWLIFELLWRDFFRFVAQKYGNKLFNRGGLLNKNFPWQEDQVRFELWRSGQTGYPLVDANMRELNLTGFMSNRGRQNVASFLCKNLGIDWRWGAEWFESCLIDYDVCSNWGNWNYTAGIGNDARDFRYFNIPKQSQQYDPQGTYLRHWLPELKNLPGDKIHQPWLLSATEQKQWGVQLGVDYPRPCVNFHQSVEARRKIE 483
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit(hide GO term definitions)

Chain A,B (CRYD_SYNY3 | P77967)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003913	DNA photolyase activity	Catalysis of the repair of a photoproduct resulting from ultraviolet irradiation of two adjacent pyrimidine residues in DNA.
biological process
	GO:0006281	DNA repair	The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
	GO:0018298	protein-chromophore linkage	The covalent or noncovalent attachment of a chromophore to a protein.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		FAD	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1np7)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1np7
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	CRYD_SYNY3 \| P77967
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	CRYD_SYNY3 \| P77967
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 1NP7)

(no "Related Entries Specified in the PDB File" available for 1NP7)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 4)

CATH Domains (3, 6)

Pfam Domains (2, 4)

Gene Ontology (6, 6)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File