1YDW - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   X-RAY STRUCTURE OF GENE PRODUCT FROM ARABIDOPSIS THALIANA AT4G09670

Authors :   G. E. Wesenberg, G. N. Phillips Jr. , E. Bitto, C. A. Bingman, S. T. M. Allard, Center For Eukaryotic Structural Genomics (Cesg)

Date :   26 Dec 04 (Deposition) - 11 Jan 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.49

Chains :   Asym./Biol. Unit : A,B

Keywords :   Structural Genomics, Protein Structure Initiative, Psi, Center For Eukaryotic Structural Genomics, Cesg, At4G09670, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Center For Eukaryotic Structural Genomics (Cesg)
X-Ray Structure Of Gene Product From Arabidopsis Thaliana At4G09670
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - AX110P-LIKE PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PVP-17
	Expression System Strain	:	B834 P(RARE2)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	AT4G09670
	Organism Common	:	THALE CRESS
	Organism Scientific	:	ARABIDOPSIS THALIANA
	Organism Taxid	:	3702

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 12)

No.	Name	Count	Type	Full Name
1	MSE	12	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 1YDW)

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

Asymmetric/Biological Unit

No.	Residues
1	Lys A:102	-	Pro A:103
2	Ala B:28	-	Pro B:29
3	Lys B:102	-	Pro B:103

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

(no "PROSITE Motif" information available for 1YDW)

(no "Exon" information available for 1YDW)

Asymmetric/Biological 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:343
 aligned with Y4967_ARATH | Q9SZ83 from UniProtKB/Swiss-Prot  Length:362

    Alignment length:355
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355     
          Y4967_ARATH     6 QIRIGVMGCADIARKVSRAIHLAPNATISGVASRSLEKAKAFATANNYPESTKIHGSYESLLEDPEIDALYVPLPTSLHVEWAIKAAEKGKHILLEKPVAMNVTEFDKIVDACEANGVQIMDGTMWVHNPRTALLKEFLSDSERFGQLKTVQSCFSFAGDEDFLKNDIRVKPGLDGLGALGDAGWYAIRATLLANNFELPKTVTAFPGAVLNEAGVILSCGASLSWEDGRTATIYCSFLANLTMEITAIGTKGTLRVHDFIIPYKETEASFTTSTKAWFNDLVTAWVSPPSEHTVKTELPQEACMVREFARLVGEIKNNGAKPDGYWPSISRKTQLVVDAVKESVDKNYQQISLS 360
               SCOP domains d1ydwa1 A:6-133,A:305-360 Probable oxidoreductase At4g09670                                                                     d1ydwa2 A:134-304 Probable oxidoreductase At4g09670                                                                                                                        d1ydwa1 A:6-13            3,A:305-360                    SCOP domains
               CATH domains 1ydwA01 A:6-133 NAD(P)-binding Rossmann-like Domain                                                                             ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhh......eee.hhhhhhhh....eeee..hhhhhhhhhhhhhh...eeee......hhhhhhhhhhhhhh....eee..hhhhhhhhh...hhhhh......eeeeeeeeeee.hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh......eeee....ee.....eeeeeeeee.....eeeeeee.eeeeeeeeeeee..eeeee..........eeeeeeee...............eeeeee...hhhhhhhhhhh...------------hhhhhhhhhhhhhhhhhhhhhh....ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ydw A   6 QIRIGVmGCADIARKVSRAIHLAPNATISGVASRSLEKAKAFATANNYPESTKIHGSYESLLEDPEIDALYVPLPTSLHVEWAIKAAEKGKHILLEKPVAmNVTEFDKIVDACEANGVQImDGTmWVHNPRTALLKEFLSDSERFGQLKTVQSCFSFAGDEDFLKNDIRVKPGLDGLGALGDAGWYAIRATLLANNFELPKTVTAFPGAVLNEAGVILSCGASLSWEDGRTATIYCSFLANLTmEITAIGTKGTLRVHDFIIPYKETEASFTTSTKAWFNDLVTAWVSPPSEHTVKTELPQEACmVREFARLV------------YWPSISRKTQLVVDAVKESVDKNYQQISLS 360
                                  | 15        25        35        45        55        65        75        85        95       105|      115       125|   |  135       145       155       165       175       185       195       205       215       225       235       245   |   255       265       275       285       295       305    |  315  |      -     | 335       345       355     
                                 12-MSE                                                                                       106-MSE             126-MSE                                                                                                                    249-MSE                                                      310-MSE 318          331                             
                                                                                                                                                      130-MSE

Chain B from PDB  Type:PROTEIN  Length:350
 aligned with Y4967_ARATH | Q9SZ83 from UniProtKB/Swiss-Prot  Length:362

    Alignment length:355
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355     
          Y4967_ARATH     6 QIRIGVMGCADIARKVSRAIHLAPNATISGVASRSLEKAKAFATANNYPESTKIHGSYESLLEDPEIDALYVPLPTSLHVEWAIKAAEKGKHILLEKPVAMNVTEFDKIVDACEANGVQIMDGTMWVHNPRTALLKEFLSDSERFGQLKTVQSCFSFAGDEDFLKNDIRVKPGLDGLGALGDAGWYAIRATLLANNFELPKTVTAFPGAVLNEAGVILSCGASLSWEDGRTATIYCSFLANLTMEITAIGTKGTLRVHDFIIPYKETEASFTTSTKAWFNDLVTAWVSPPSEHTVKTELPQEACMVREFARLVGEIKNNGAKPDGYWPSISRKTQLVVDAVKESVDKNYQQISLS 360
               SCOP domains d1ydwb1 B:6-133,B:305-360 Probable oxidoreductase At4g09670                                                                     d1ydwb2 B:134-304 Probable oxidoreductase At4g09670                                                                                                                        d1ydwb1 B:6     -133,B:305-360                           SCOP domains
               CATH domains 1ydwB01 B:6-133 NAD(P)-binding Rossmann-like Domain                                                                             ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhh......eee.hhhhhhh.....eeee..hhhhhhhhhhhhhh...eeee......hhhhhhhhhhhhhhh...eee..hhhhhhhhhhhhhhhhh......eeeeeeeeeee.hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh......eeee....ee.....eeeeeeeee.....eeeeeee.eeeeeeeeeeee..eeeee..........eeeeeeee...............eeeeee...hhhhhhhhhhh-----.........hhhhhhhhhhhhhhhhhhhhhhh....ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ydw B   6 QIRIGVmGCADIARKVSRAIHLAPNATISGVASRSLEKAKAFATANNYPESTKIHGSYESLLEDPEIDALYVPLPTSLHVEWAIKAAEKGKHILLEKPVAmNVTEFDKIVDACEANGVQImDGTmWVHNPRTALLKEFLSDSERFGQLKTVQSCFSFAGDEDFLKNDIRVKPGLDGLGALGDAGWYAIRATLLANNFELPKTVTAFPGAVLNEAGVILSCGASLSWEDGRTATIYCSFLANLTmEITAIGTKGTLRVHDFIIPYKETEASFTTSTKAWFNDLVTAWVSPPSEHTVKTELPQEACmVREFA-----IKNNGAKPDGYWPSISRKTQLVVDAVKESVDKNYQQISLS 360
                                  | 15        25        35        45        55        65        75        85        95       105|      115       125|   |  135       145       155       165       175       185       195       205       215       225       235       245   |   255       265       275       285       295       305    |  315     | 325       335       345       355     
                                 12-MSE                                                                                       106-MSE             126-MSE                                                                                                                    249-MSE                                                      310-MSE5   321                                       
                                                                                                                                                      130-MSE

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/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: NAD(P)-binding Rossmann-like Domain (1244)

Thale cress (Arabidopsis thaliana) (15)

1a	1ydwA01	A:6-133
1b	1ydwB01	B:6-133

(no "Pfam Domain" information available for 1YDW)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (Y4967_ARATH | Q9SZ83)

molecular function
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric/Biological Unit
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		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
(no "Sites" information available for 1ydw)

	Cis Peptide Bonds
		Ala B:28 - Pro B:29	[ RasMol ]
		Lys A:102 - Pro A:103	[ RasMol ]
		Lys B:102 - Pro B:103	[ RasMol ]

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	Y4967_ARATH \| Q9SZ83	:	2q4e

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Description

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Chains, Units

Ligands, Modified Residues, Ions (1, 12)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

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Exons (0, 0)

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