3K1Y - JenaLib

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Title :   X-RAY STRUCTURE OF OXIDOREDUCTASE FROM CORYNEBACTERIUM DIPHTHERIAE. ORTHOROMBIC CRYSTAL FORM, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET CDR100D

Authors :   A. Kuzin, S. Lew, S. Sahdev, R. Xiao, C. Ciccosanti, H. Wang, J. K. Everett, R. Nair, T. B. Acton, B. Rost, G. T. Montelione, L. Tong, J. F. Hunt, Northeast Structural Genomics Consortium (Nesg)

Date :   29 Sep 09 (Deposition) - 20 Oct 09 (Release) - 20 Oct 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,F  (1x)
Biol. Unit 2: D,E  (2x)

Keywords :   Crystal Structure, Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Cdr100D, Q6Ngs1, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Kuzin, S. Lew, J. Seetharaman, S. Sahdev, R. Xiao, C. Ciccosanti, H. Wang, J. K. Everett, R. Nair, T. B. Acton, B. Rost, G. T. Montelione, L. Tong, J. F. Hunt
Northeast Structural Genomics Consortium Target Cdr100D
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - OXIDOREDUCTASE
	Chains	:	A, B, C, D, E, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET 14-15
	Expression System Strain	:	BL21(DE3)+ MAGIC
	Expression System Taxid	:	469008
	Expression System Vector Type	:	CPLASMID
	Gene	:	DIP1437
	Organism Scientific	:	CORYNEBACTERIUM DIPHTHERIAE
	Organism Taxid	:	1717

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A	B	C			F
Biological Unit 2 (2x)	:				D	E

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 52)

No.	Name	Count	Type	Full Name
1	MSE	36	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	16	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 34)

No.	Name	Count	Type	Full Name
1	MSE	24	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	10	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 36)

No.	Name	Count	Type	Full Name
1	MSE	24	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	12	Ligand/Ion	SULFATE ION

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLY A:10 , LEU A:11 , SER A:12 , SER A:15 , SER A:16 , THR A:17	BINDING SITE FOR RESIDUE SO4 A 182
02	AC2	SOFTWARE	GLY A:118 , SER A:119 , ARG A:121	BINDING SITE FOR RESIDUE SO4 A 183
03	AC3	SOFTWARE	ARG A:167 , THR E:13	BINDING SITE FOR RESIDUE SO4 A 184
04	AC4	SOFTWARE	THR A:63 , THR A:64 , GLY C:36	BINDING SITE FOR RESIDUE SO4 A 185
05	AC5	SOFTWARE	GLY B:10 , LEU B:11 , SER B:12 , SER B:15 , SER B:16 , THR B:17	BINDING SITE FOR RESIDUE SO4 B 182
06	AC6	SOFTWARE	PHE B:86 , LYS B:87	BINDING SITE FOR RESIDUE SO4 B 183
07	AC7	SOFTWARE	THR C:63 , THR C:64	BINDING SITE FOR RESIDUE SO4 C 182
08	AC8	SOFTWARE	GLY C:10 , LEU C:11 , SER C:12 , PRO C:14 , SER C:15 , SER C:16 , THR C:17	BINDING SITE FOR RESIDUE SO4 C 183
09	AC9	SOFTWARE	GLY D:10 , LEU D:11 , SER D:12 , SER D:15 , SER D:16 , THR D:17 , HOH D:209	BINDING SITE FOR RESIDUE SO4 D 182
10	BC1	SOFTWARE	GLY D:118 , SER D:119 , ARG D:121 , HIS D:122 , HOH D:220	BINDING SITE FOR RESIDUE SO4 D 183
11	BC2	SOFTWARE	TYR D:136 , HIS E:122 , ARG E:164	BINDING SITE FOR RESIDUE SO4 D 184
12	BC3	SOFTWARE	GLY E:10 , LEU E:11 , SER E:12 , SER E:15 , SER E:16 , THR E:17 , PRO E:84	BINDING SITE FOR RESIDUE SO4 E 182
13	BC4	SOFTWARE	TYR D:136 , LYS E:87	BINDING SITE FOR RESIDUE SO4 E 183
14	BC5	SOFTWARE	ALA E:117 , GLY E:118 , SER E:119 , ARG E:121 , HIS E:122	BINDING SITE FOR RESIDUE SO4 E 184
15	BC6	SOFTWARE	GLY F:10 , LEU F:11 , SER F:12 , SER F:15 , SER F:16 , THR F:17 , PRO F:84	BINDING SITE FOR RESIDUE SO4 F 182
16	BC7	SOFTWARE	GLY F:118 , SER F:119 , ARG F:121 , HOH F:201	BINDING SITE FOR RESIDUE SO4 F 183

(no "SS Bond" information available for 3K1Y)

Asymmetric Unit

No.	Residues
1	Thr A:13	-	Pro A:14
2	Thr B:13	-	Pro B:14
3	Thr C:13	-	Pro C:14
4	Thr D:13	-	Pro D:14
5	Thr E:13	-	Pro E:14
6	Thr F:13	-	Pro F:14

(no "SAP(SNP)/Variant" information available for 3K1Y)

(no "PROSITE Motif" information available for 3K1Y)

(no "Exon" information available for 3K1Y)

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:182
 aligned with Q6NGS1_CORDI | Q6NGS1 from UniProtKB/TrEMBL  Length:221

    Alignment length:182
                              1                                                                                                                                                                                   
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178  
         Q6NGS1_CORDI     - --MRTLAVISAGLSTPSSTRQIADSISEAVTAAVSARGEALSVSTIELSELIPDLMTAMTTRVHTTKLEEITSALSASDGLVVATPVFKASYTGLFKMFFDILDTDALTGMPTIIAATAGSARHSLVLDYALRPLLSYMRAVVVPTGVFAATEDFGGPEGAEFNKRIARAAGELASLIVEES 180
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee......hhhhhhhhhhhhhhhhhhhhh...eeeeeee...hhhhhh........hhhhhhhhhhhhhh.eeeeeee......hhhhhhhhhhh........eeeeeeee......hhhhhhhhhhhhhh..ee....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k1y A  -1 SHmRTLAVISAGLSTPSSTRQIADSISEAVTAAVSARGEALSVSTIELSELIPDLmTAmTTRVHTTKLEEITSALSASDGLVVATPVFKASYTGLFKmFFDILDTDALTGmPTIIAATAGSARHSLVLDYALRPLLSYmRAVVVPTGVFAATEDFGGPEGAEFNKRIARAAGELASLIVEES 180
                              |      8        18        28        38        48     |  58        68        78        88       |98       108|      118       128       138       148       158       168       178  
                              |                                                   54-MSE                                    96-MSE      109-MSE                     137-MSE                                       
                              1-MSE                                                  57-MSE

Chain B from PDB  Type:PROTEIN  Length:180
 aligned with Q6NGS1_CORDI | Q6NGS1 from UniProtKB/TrEMBL  Length:221

    Alignment length:180
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
         Q6NGS1_CORDI     1 MRTLAVISAGLSTPSSTRQIADSISEAVTAAVSARGEALSVSTIELSELIPDLMTAMTTRVHTTKLEEITSALSASDGLVVATPVFKASYTGLFKMFFDILDTDALTGMPTIIAATAGSARHSLVLDYALRPLLSYMRAVVVPTGVFAATEDFGGPEGAEFNKRIARAAGELASLIVEES 180
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee......hhhhhhhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhh...hhhhhhhhhhhh...eeeeeeeee..eehhhhhhhhhhh........eeeeeeee......hhhhhhhhhhhhhh..ee....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3k1y B   1 mRTLAVISAGLSTPSSTRQIADSISEAVTAAVSARGEALSVSTIELSELIPDLmTAmTTRVHTTKLEEITSALSASDGLVVATPVFKASYTGLFKmFFDILDTDALTGmPTIIAATAGSARHSLVLDYALRPLLSYmRAVVVPTGVFAATEDFGGPEGAEFNKRIARAAGELASLIVEES 180
                            |       10        20        30        40        50   |  | 60        70        80        90     | 100       110       120       130      |140       150       160       170       180
                            1-MSE                                               54-MSE                                    96-MSE      109-MSE                     137-MSE                                       
                                                                                   57-MSE

Chain C from PDB  Type:PROTEIN  Length:181
 aligned with Q6NGS1_CORDI | Q6NGS1 from UniProtKB/TrEMBL  Length:221

    Alignment length:181
                             1                                                                                                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179 
         Q6NGS1_CORDI     - -MRTLAVISAGLSTPSSTRQIADSISEAVTAAVSARGEALSVSTIELSELIPDLMTAMTTRVHTTKLEEITSALSASDGLVVATPVFKASYTGLFKMFFDILDTDALTGMPTIIAATAGSARHSLVLDYALRPLLSYMRAVVVPTGVFAATEDFGGPEGAEFNKRIARAAGELASLIVEES 180
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee......hhhhhhhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhh...hhhhhhhhhhhhhh.eeeee........hhhhhhhhhhh........eeeeeeee......hhhhhhhhhhhhhh..ee....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k1y C   0 HmRTLAVISAGLSTPSSTRQIADSISEAVTAAVSARGEALSVSTIELSELIPDLmTAmTTRVHTTKLEEITSALSASDGLVVATPVFKASYTGLFKmFFDILDTDALTGmPTIIAATAGSARHSLVLDYALRPLLSYmRAVVVPTGVFAATEDFGGPEGAEFNKRIARAAGELASLIVEES 180
                             |       9        19        29        39        49    |  |59        69        79        89      | 99       109       119       129       139       149       159       169       179 
                             1-MSE                                               54-MSE                                    96-MSE      109-MSE                     137-MSE                                       
                                                                                    57-MSE

Chain D from PDB  Type:PROTEIN  Length:182
 aligned with Q6NGS1_CORDI | Q6NGS1 from UniProtKB/TrEMBL  Length:221

    Alignment length:182
                              1                                                                                                                                                                                   
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178  
         Q6NGS1_CORDI     - --MRTLAVISAGLSTPSSTRQIADSISEAVTAAVSARGEALSVSTIELSELIPDLMTAMTTRVHTTKLEEITSALSASDGLVVATPVFKASYTGLFKMFFDILDTDALTGMPTIIAATAGSARHSLVLDYALRPLLSYMRAVVVPTGVFAATEDFGGPEGAEFNKRIARAAGELASLIVEES 180
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee......hhhhhhhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhh...hhhhhhhhhhhhh..eeeeeeeee..eehhhhhhhhhhh........eeeeeeee....hhhhh..hhhhhhhhh..ee....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k1y D  -1 SHmRTLAVISAGLSTPSSTRQIADSISEAVTAAVSARGEALSVSTIELSELIPDLmTAmTTRVHTTKLEEITSALSASDGLVVATPVFKASYTGLFKmFFDILDTDALTGmPTIIAATAGSARHSLVLDYALRPLLSYmRAVVVPTGVFAATEDFGGPEGAEFNKRIARAAGELASLIVEES 180
                              |      8        18        28        38        48     |  58        68        78        88       |98       108|      118       128       138       148       158       168       178  
                              1-MSE                                               54-MSE                                    96-MSE      109-MSE                     137-MSE                                       
                                                                                     57-MSE

Chain E from PDB  Type:PROTEIN  Length:180
 aligned with Q6NGS1_CORDI | Q6NGS1 from UniProtKB/TrEMBL  Length:221

    Alignment length:180
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
         Q6NGS1_CORDI     1 MRTLAVISAGLSTPSSTRQIADSISEAVTAAVSARGEALSVSTIELSELIPDLMTAMTTRVHTTKLEEITSALSASDGLVVATPVFKASYTGLFKMFFDILDTDALTGMPTIIAATAGSARHSLVLDYALRPLLSYMRAVVVPTGVFAATEDFGGPEGAEFNKRIARAAGELASLIVEES 180
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee......hhhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhhh....hhhhhhhhhhhh...eeeeeee......hhhhhhhhhhh........eeeeeeee......hhhhhhhhhhhhhh..ee....eeee.hhh.hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3k1y E   1 mRTLAVISAGLSTPSSTRQIADSISEAVTAAVSARGEALSVSTIELSELIPDLmTAmTTRVHTTKLEEITSALSASDGLVVATPVFKASYTGLFKmFFDILDTDALTGmPTIIAATAGSARHSLVLDYALRPLLSYmRAVVVPTGVFAATEDFGGPEGAEFNKRIARAAGELASLIVEES 180
                            |       10        20        30        40        50   |  | 60        70        80        90     | 100       110       120       130      |140       150       160       170       180
                            1-MSE                                               54-MSE                                    96-MSE      109-MSE                     137-MSE                                       
                                                                                   57-MSE

Chain F from PDB  Type:PROTEIN  Length:180
 aligned with Q6NGS1_CORDI | Q6NGS1 from UniProtKB/TrEMBL  Length:221

    Alignment length:180
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
         Q6NGS1_CORDI     1 MRTLAVISAGLSTPSSTRQIADSISEAVTAAVSARGEALSVSTIELSELIPDLMTAMTTRVHTTKLEEITSALSASDGLVVATPVFKASYTGLFKMFFDILDTDALTGMPTIIAATAGSARHSLVLDYALRPLLSYMRAVVVPTGVFAATEDFGGPEGAEFNKRIARAAGELASLIVEES 180
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) FMN_red-3k1yF01 F:1-154                                                                                                                                   -------------------------- Pfam domains (1)
           Pfam domains (2) FMN_red-3k1yF02 F:1-154                                                                                                                                   -------------------------- Pfam domains (2)
           Pfam domains (3) FMN_red-3k1yF03 F:1-154                                                                                                                                   -------------------------- Pfam domains (3)
           Pfam domains (4) FMN_red-3k1yF04 F:1-154                                                                                                                                   -------------------------- Pfam domains (4)
           Pfam domains (5) FMN_red-3k1yF05 F:1-154                                                                                                                                   -------------------------- Pfam domains (5)
           Pfam domains (6) FMN_red-3k1yF06 F:1-154                                                                                                                                   -------------------------- Pfam domains (6)
         Sec.struct. author .eeeeeee......hhhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhhhh...hhhhhhhhhhhhhh.eeeeeeeee..eehhhhhhhhhh.........eeeeeeee......hhhhhhhhhhhhhh..ee....eeee....hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3k1y F   1 mRTLAVISAGLSTPSSTRQIADSISEAVTAAVSARGEALSVSTIELSELIPDLmTAmTTRVHTTKLEEITSALSASDGLVVATPVFKASYTGLFKmFFDILDTDALTGmPTIIAATAGSARHSLVLDYALRPLLSYmRAVVVPTGVFAATEDFGGPEGAEFNKRIARAAGELASLIVEES 180
                            |       10        20        30        40        50   |  | 60        70        80        90     | 100       110       120       130      |140       150       160       170       180
                            1-MSE                                               54-MSE                                    96-MSE      109-MSE                     137-MSE                                       
                                                                                   57-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 '\|'

(no "SCOP Domain" information available for 3K1Y)

(no "CATH Domain" information available for 3K1Y)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Flavoprotein (71)

Family: FMN_red (5)

Corynebacterium diphtheriae (2)

1a	FMN_red-3k1yF01	F:1-154
1b	FMN_red-3k1yF02	F:1-154
1c	FMN_red-3k1yF03	F:1-154
1d	FMN_red-3k1yF04	F:1-154
1e	FMN_red-3k1yF05	F:1-154
1f	FMN_red-3k1yF06	F:1-154

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (Q6NGS1_CORDI | Q6NGS1)

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.

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		Thr A:13 - Pro A:14	[ RasMol ]
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		Thr C:13 - Pro C:14	[ RasMol ]
		Thr D:13 - Pro D:14	[ RasMol ]
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2vzj	36% OF AMINO ACID RESIDUES ARE IDENTICAL. RELATED ID: CDR100D RELATED DB: TARGETDB

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 52)

Sites (16, 16)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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