3UCE - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Biological Unit 5 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A SMALL-CHAIN DEHYDROGENASE IN COMPLEX WITH NADPH

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

Date :   26 Oct 11 (Deposition) - 28 Nov 12 (Release) - 13 Mar 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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 :   Rossmann Fold, Small-Chain Dehydrogenase, 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	:	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)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	NDP	4	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	NDP	4	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	NDP	2	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	NDP	2	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

Biological Unit 4 (1, 2)

No.	Name	Count	Type	Full Name
1	NDP	2	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

Biological Unit 5 (1, 2)

No.	Name	Count	Type	Full Name
1	NDP	2	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:13 , THR A:15 , SER A:16 , GLY A:17 , ILE A:18 , SER A:37 , ARG A:38 , GLN A:39 , LEU A:42 , ASP A:43 , ILE A:44 , THR A:66 , ALA A:67 , GLY A:68 , SER A:69 , THR A:90 , LYS A:91 , THR A:115 , SER A:116 , PRO A:158 , GLY A:159 , LEU A:160 , THR A:161 , THR A:163 , ALA A:165 , TYR A:166 , HOH A:236 , HOH A:247 , HOH A:273 , HOH A:449 , HOH A:914 , HOH A:988	BINDING SITE FOR RESIDUE NDP A 500
2	AC2	SOFTWARE	GLY B:13 , THR B:15 , SER B:16 , GLY B:17 , ILE B:18 , SER B:37 , ARG B:38 , GLN B:39 , LEU B:42 , ASP B:43 , ILE B:44 , THR B:66 , ALA B:67 , GLY B:68 , SER B:69 , THR B:90 , LYS B:91 , THR B:115 , SER B:116 , PRO B:158 , GLY B:159 , LEU B:160 , THR B:161 , THR B:163 , ALA B:165 , TYR B:166 , HOH B:224 , HOH B:252 , HOH B:280 , HOH B:484 , HOH B:989	BINDING SITE FOR RESIDUE NDP B 500
3	AC3	SOFTWARE	GLY C:13 , THR C:15 , SER C:16 , GLY C:17 , ILE C:18 , SER C:37 , ARG C:38 , GLN C:39 , LEU C:42 , ASP C:43 , ILE C:44 , THR C:66 , ALA C:67 , GLY C:68 , SER C:69 , THR C:90 , LYS C:91 , THR C:115 , SER C:116 , PRO C:158 , GLY C:159 , LEU C:160 , THR C:161 , THR C:163 , GLU C:164 , ALA C:165 , TYR C:166 , HOH C:235 , HOH C:249 , HOH C:265 , HOH C:458	BINDING SITE FOR RESIDUE NDP C 500
4	AC4	SOFTWARE	GLY D:13 , THR D:15 , SER D:16 , GLY D:17 , ILE D:18 , SER D:37 , ARG D:38 , GLN D:39 , LEU D:42 , ASP D:43 , ILE D:44 , THR D:66 , ALA D:67 , GLY D:68 , SER D:69 , THR D:90 , LYS D:91 , THR D:115 , SER D:116 , PRO D:158 , GLY D:159 , LEU D:160 , THR D:161 , THR D:163 , ALA D:165 , TYR D:166 , HOH D:226 , HOH D:239 , HOH D:270 , HOH D:486 , HOH D:612 , HOH D:676 , HOH D:733 , HOH D:987	BINDING SITE FOR RESIDUE NDP D 500

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

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 3UCE)

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

(no "Exon" information available for 3UCE)

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:219
 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 d3ucea_ 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....hhhhh..hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh......eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3uce A   5 DKTVYVVLGGTSGIGAELAKQLESEHTIVHVASRQTGLDISDEKSVYHYFETIGAFDHLIVTAGSYAPAGKVVDVEVTQAKYAFDTKFWGAVLAAKHGARYLKQGGSITLTSGMLSRKVVANTYVKAAINAAIEATTKVLAKELAPIRVNAISPGLTKTEAYKGMNADDRDAMYQRTQSHLPVGKVGEASDIAMAYLFAIQNSYMTGTVIDVDGGALLG 223
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214

Chain B from PDB  Type:PROTEIN  Length:219
 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 d3uceb_ 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....hhhhh..hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh......eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3uce B   5 DKTVYVVLGGTSGIGAELAKQLESEHTIVHVASRQTGLDISDEKSVYHYFETIGAFDHLIVTAGSYAPAGKVVDVEVTQAKYAFDTKFWGAVLAAKHGARYLKQGGSITLTSGMLSRKVVANTYVKAAINAAIEATTKVLAKELAPIRVNAISPGLTKTEAYKGMNADDRDAMYQRTQSHLPVGKVGEASDIAMAYLFAIQNSYMTGTVIDVDGGALLG 223
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214

Chain C from PDB  Type:PROTEIN  Length:219
 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 d3ucec_ 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..eehhhhh..hhhhhhhhhhhhhhhh.....eehhhhhhhhhhhhhh......eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3uce C   5 DKTVYVVLGGTSGIGAELAKQLESEHTIVHVASRQTGLDISDEKSVYHYFETIGAFDHLIVTAGSYAPAGKVVDVEVTQAKYAFDTKFWGAVLAAKHGARYLKQGGSITLTSGMLSRKVVANTYVKAAINAAIEATTKVLAKELAPIRVNAISPGLTKTEAYKGMNADDRDAMYQRTQSHLPVGKVGEASDIAMAYLFAIQNSYMTGTVIDVDGGALLG 223
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214

Chain D from PDB  Type:PROTEIN  Length:219
 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 d3uced_ 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....hhhhh..hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh......eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3uce D   5 DKTVYVVLGGTSGIGAELAKQLESEHTIVHVASRQTGLDISDEKSVYHYFETIGAFDHLIVTAGSYAPAGKVVDVEVTQAKYAFDTKFWGAVLAAKHGARYLKQGGSITLTSGMLSRKVVANTYVKAAINAAIEATTKVLAKELAPIRVNAISPGLTKTEAYKGMNADDRDAMYQRTQSHLPVGKVGEASDIAMAYLFAIQNSYMTGTVIDVDGGALLG 223
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214

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	d3ucea_	A:
1b	d3uceb_	B:
1c	d3ucec_	C:
1d	d3uced_	D:

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

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

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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	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 ]

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Description

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Ligands, Modified Residues, Ions (1, 4)

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