3UCF - JenaLib

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Biological Unit 5 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A SMALL-CHAIN DEHYDROGENASE

Authors :   G. Buysschaert, K. Verstraete, S. Savvides, B. Vergauwen

Date :   26 Oct 11 (Deposition) - 30 Jan 13 (Release) - 13 Mar 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.35

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D  (1x)
Biol. Unit 2: A,C  (1x)
Biol. Unit 3: A,B  (1x)
Biol. Unit 4: B,D  (1x)
Biol. Unit 5: C,D  (1x)

Keywords :   Small-Chain Dehydrogenase Rossmann Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Buysschaert, K. Verstraete, S. N. Savvides, B. Vergauwen
Structural And Biochemical Characterization Of An Atypical Short-Chain Dehydrogenase/Reductase Reveals An Unusual Cofactor Preference.
Febs J. V. 280 1358 2013
PubMed-ID: 23311896 | Reference-DOI: 10.1111/FEBS.12128

Molecule 1 - DEHYDROGENASE
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PACYCDUET-I
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	VVA-1599, VVA1599
	Organism Scientific	:	VIBRIO VULNIFICUS
	Organism Taxid	:	196600
	Strain	:	YJ016

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3UCF)

(no "Site" information available for 3UCF)

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

Asymmetric Unit

No.	Residues
1	Ala A:149	-	Pro A:150
2	Ala B:149	-	Pro B:150
3	Ala C:149	-	Pro C:150
4	Ala D:149	-	Pro D:150

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

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

(no "Exon" information available for 3UCF)

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:187
 aligned with Q7MBY8_VIBVY | Q7MBY8 from UniProtKB/TrEMBL  Length:223

    Alignment length:219
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214         
         Q7MBY8_VIBVY     5 DKTVYVVLGGTSGIGAELAKQLESEHTIVHVASRQTGLDISDEKSVYHYFETIGAFDHLIVTAGSYAPAGKVVDVEVTQAKYAFDTKFWGAVLAAKHGARYLKQGGSITLTSGMLSRKVVANTYVKAAINAAIEATTKVLAKELAPIRVNAISPGLTKTEAYKGMNADDRDAMYQRTQSHLPVGKVGEASDIAMAYLFAIQNSYMTGTVIDVDGGALLG 223
               SCOP domains d3ucfa_ A: automated matches                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...hhhhhhhhhhhh...eeeeeehhhhh....hhhhhhhhhhhhh.eeeeee..--..........hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh..eeeeeee..------------------------------.hhhhhhhhhhhhhhh......eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ucf A   5 DKTVYVVLGGTSGIGAELAKQLESEHTIVHVASRQTGLDISDEKSVYHYFETIGAFDHLIVTA--YAPAGKVVDVEVTQAKYAFDTKFWGAVLAAKHGARYLKQGGSITLTSGMLSRKVVANTYVKAAINAAIEATTKVLAKELAPIRVNAISPGL------------------------------GEASDIAMAYLFAIQNSYMTGTVIDVDGGALLG 223
                                    14        24        34        44        54        64  |  |  74        84        94       104       114       124       134       144       154     |   -         -         -      |194       204       214         
                                                                                         67 70                                                                                       160                            191

Chain B from PDB  Type:PROTEIN  Length:195
 aligned with Q7MBY8_VIBVY | Q7MBY8 from UniProtKB/TrEMBL  Length:223

    Alignment length:219
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214         
         Q7MBY8_VIBVY     5 DKTVYVVLGGTSGIGAELAKQLESEHTIVHVASRQTGLDISDEKSVYHYFETIGAFDHLIVTAGSYAPAGKVVDVEVTQAKYAFDTKFWGAVLAAKHGARYLKQGGSITLTSGMLSRKVVANTYVKAAINAAIEATTKVLAKELAPIRVNAISPGLTKTEAYKGMNADDRDAMYQRTQSHLPVGKVGEASDIAMAYLFAIQNSYMTGTVIDVDGGALLG 223
               SCOP domains d3ucfb_ B: automated matches                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...hhhhhhhhhhhh...eeeeeehhhhh....hhhhhhhhhhhhh.eeeeee..............hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh..eeeeeee..------------------------.......hhhhhhhhhhhhhhh......eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ucf B   5 DKTVYVVLGGTSGIGAELAKQLESEHTIVHVASRQTGLDISDEKSVYHYFETIGAFDHLIVTAGSYAPAGKVVDVEVTQAKYAFDTKFWGAVLAAKHGARYLKQGGSITLTSGMLSRKVVANTYVKAAINAAIEATTKVLAKELAPIRVNAISPGL------------------------LPVGKVGEASDIAMAYLFAIQNSYMTGTVIDVDGGALLG 223
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154     |   -         -         -|      194       204       214         
                                                                                                                                                                                     160                      185

Chain C from PDB  Type:PROTEIN  Length:208
 aligned with Q7MBY8_VIBVY | Q7MBY8 from UniProtKB/TrEMBL  Length:223

    Alignment length:219
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214         
         Q7MBY8_VIBVY     5 DKTVYVVLGGTSGIGAELAKQLESEHTIVHVASRQTGLDISDEKSVYHYFETIGAFDHLIVTAGSYAPAGKVVDVEVTQAKYAFDTKFWGAVLAAKHGARYLKQGGSITLTSGMLSRKVVANTYVKAAINAAIEATTKVLAKELAPIRVNAISPGLTKTEAYKGMNADDRDAMYQRTQSHLPVGKVGEASDIAMAYLFAIQNSYMTGTVIDVDGGALLG 223
               SCOP domains d3ucfc_ C: automated matches                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...hhhhhhhhhhhh...eeeeeehhhhh....hhhhhhhhhhhhh.eeeeee..............hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh..eeeeeee....-----------.hhhhhhhhhhh......hhhhhhhhhhhhhhh......eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ucf C   5 DKTVYVVLGGTSGIGAELAKQLESEHTIVHVASRQTGLDISDEKSVYHYFETIGAFDHLIVTAGSYAPAGKVVDVEVTQAKYAFDTKFWGAVLAAKHGARYLKQGGSITLTSGMLSRKVVANTYVKAAINAAIEATTKVLAKELAPIRVNAISPGLTK-----------RDAMYQRTQSHLPVGKVGEASDIAMAYLFAIQNSYMTGTVIDVDGGALLG 223
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       | -       174       184       194       204       214         
                                                                                                                                                                                       162         174

Chain D from PDB  Type:PROTEIN  Length:186
 aligned with Q7MBY8_VIBVY | Q7MBY8 from UniProtKB/TrEMBL  Length:223

    Alignment length:218
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214        
         Q7MBY8_VIBVY     5 DKTVYVVLGGTSGIGAELAKQLESEHTIVHVASRQTGLDISDEKSVYHYFETIGAFDHLIVTAGSYAPAGKVVDVEVTQAKYAFDTKFWGAVLAAKHGARYLKQGGSITLTSGMLSRKVVANTYVKAAINAAIEATTKVLAKELAPIRVNAISPGLTKTEAYKGMNADDRDAMYQRTQSHLPVGKVGEASDIAMAYLFAIQNSYMTGTVIDVDGGALL 222
               SCOP domains d3ucfd_ D: automated matches                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...hhhhhhhhhhhh...eeeeeehhhhh....hhhhhhhhhhhhh.eeeeee..............hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.--------------------------------.hhhhhhhhhhhhhh......eeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ucf D   5 DKTVYVVLGGTSGIGAELAKQLESEHTIVHVASRQTGLDISDEKSVYHYFETIGAFDHLIVTAGSYAPAGKVVDVEVTQAKYAFDTKFWGAVLAAKHGARYLKQGGSITLTSGMLSRKVVANTYVKAAINAAIEATTKVLAKELAPIRVNAISPG--------------------------------EASDIAMAYLFAIQNSYMTGTVIDVDGGALL 222
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154    |    -         -         -       194       204       214        
                                                                                                                                                                                    159                              192

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

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: NAD(P)-binding Rossmann-fold domains (1604)

Superfamily: NAD(P)-binding Rossmann-fold domains (1604)

Family: automated matches (447)

Protein domain: automated matches (447)

Vibrio vulnificus [TaxId: 196600] (2)

1a	d3ucfa_	A:
1b	d3ucfb_	B:
1c	d3ucfc_	C:
1d	d3ucfd_	D:

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

(no "Pfam Domain" information available for 3UCF)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (Q7MBY8_VIBVY | Q7MBY8)

molecular function
	GO:0042802		identical protein binding		Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0000166		nucleotide binding		Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3ucf)

	Sites
(no "Sites" information available for 3ucf)

	Cis Peptide Bonds
		Ala A:149 - Pro A:150	[ RasMol ]
		Ala B:149 - Pro B:150	[ RasMol ]
		Ala C:149 - Pro C:150	[ RasMol ]
		Ala D:149 - Pro D:150	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
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		Biological Unit 4	[ Jena3D ]
		Biological Unit 5	[ Jena3D ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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