2ZUQ - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF DSBB-FAB COMPLEX

Authors :   K. Inaba, M. Suzuki, S. Murakami

Date :   28 Oct 08 (Deposition) - 14 Apr 09 (Release) - 14 Apr 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.30

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

Keywords :   Disulfide Bond, Membrane Protein, Fab, E. Coli, Cell Inner Membrane, Cell Membrane, Chaperone, Electron Transport, Membrane, Oxidoreductase, Redox-Active Center, Transmembrane, Transport, Oxidoreductase/Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Inaba, S. Murakami, A. Nakagawa, H. Iida, M. Kinjo, K. Ito, M. Suzuki
Dynamic Nature Of Disulphide Bond Formation Catalysts Revealed By Crystal Structures Of Dsbb
Embo J. V. 28 779 2009
PubMed-ID: 19214188 | Reference-DOI: 10.1038/EMBOJ.2009.21
(for further references see the PDB file header)

Molecule 1 - DISULFIDE BOND FORMATION PROTEIN B
	Chains	:	A, D
	EC Number	:	1.8.5.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQE70
	Expression System Strain	:	M15
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	DSBB
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12
	Synonym	:	DSBB, DISULFIDE OXIDOREDUCTASE

Molecule 2 - FAB FRAGMENT LIGHT CHAIN
	Chains	:	B, E
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	FAB FRAGMENT IS OBTAINED BY PAPAIN DIGESTION OF A SELECTED MONOCLONAL ANTIBODY.

Molecule 3 - FAB FRAGMENT HEAVY CHAIN
	Chains	:	C, F
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	FAB FRAGMENT IS OBTAINED BY PAPAIN DIGESTION OF A SELECTED MONOCLONAL ANTIBODY.

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	UQ1	2	Ligand/Ion	UBIQUINONE-1

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	UQ1	1	Ligand/Ion	UBIQUINONE-1

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	UQ1	1	Ligand/Ion	UBIQUINONE-1

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:25 , ALA A:29 , GLN A:33 , PRO A:40 , SER A:41 , CYS A:44 , GLU A:47 , MET A:142 , PRO A:143 , LEU A:146	BINDING SITE FOR RESIDUE UQ1 A 177
2	AC2	SOFTWARE	LEU D:25 , ALA D:29 , PHE D:32 , LEU D:38 , CYS D:44 , ARG D:48 , MET D:142 , PRO D:143 , LEU D:146	BINDING SITE FOR RESIDUE UQ1 D 177

Asymmetric Unit

No.	Residues
1	A:104	-	A:130
2	B:43	-	B:114
3	B:159	-	B:219
4	B:239	-	C:134
5	C:22	-	C:96
6	C:146	-	C:201
7	D:104	-	D:130
8	E:43	-	E:114
9	E:159	-	E:219
10	E:239	-	F:134
11	F:22	-	F:96
12	F:146	-	F:201

Asymmetric Unit

No.	Residues
1	Leu A:37	-	Leu A:38
2	Pro A:65	-	Lys A:66
3	Ser B:27	-	Pro B:28
4	Tyr B:165	-	Pro B:166
5	Phe C:152	-	Pro C:153
6	Glu C:154	-	Pro C:155
7	Leu D:37	-	Leu D:38
8	Pro D:65	-	Lys D:66
9	Ser E:27	-	Pro E:28
10	Arg E:53	-	Thr E:54
11	Tyr E:165	-	Pro E:166
12	Phe F:152	-	Pro F:153
13	Glu F:154	-	Pro F:155

(no "SAP(SNP)/Variant" information available for 2ZUQ)

(no "PROSITE Motif" information available for 2ZUQ)

(no "Exon" information available for 2ZUQ)

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:148
 aligned with DSBB_ECOLI | P0A6M2 from UniProtKB/Swiss-Prot  Length:176

    Alignment length:153
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159   
           DSBB_ECOLI    10 QGRGAWLLMAFTALALELTALWFQHVMLLKPCVLCIYERCALFGVLGAALIGAIAPKTPLRYVAMVIWLYSAFRGVQLTYEHTMLQLYPSPFATCDFMVRFPEWLPLDKWVPQVFVASGDCAERQWDFLGLEMPQWLLGIFIAYLIVAVLVVI 162
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........-----...........................hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zuq A  10 QGRGAWLLMAFTALALELTALWFQHVMLLKPSVLCIYERVALFGVLGAALIGAIAPKTPLRYVAMVIWLYSAFRGVQLTYEHTMLQLYPSPFATCDFMV-----LPLDKWVPQVFVASGDCAERQWDFLGLEMPQWLLGIFIAYLIVAVLVVI 162
                                    19        29        39        49        59        69        79        89        99        |-    |  119       129       139       149       159   
                                                                                                                            108   114

Chain B from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------2zuqB02 B:134-236 Immunoglobulins                                                                      --- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.............eeeeee......eeee.............eeeee...eeeeee........eeeeeee.....ee....eeee......eeeee..hhhhhhh.eeeeeeeee.........eeee........ee...............eeeeeee.hhhhhh.eeeee..........eeeee.hhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zuq B  21 DIVMSQSPSSLAVSAGEKVTMSCKSSQSLLNSRTRKNYLAWYQQKPGQSPKLLIYWASTRESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYCKQSYNLYTFGGGTKLEIKADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 239
                                    30        40        50        60        70        80        90       100       110       120       130 ||    141       151       161       171       181       191       201       211       221       231        
                                                                                                                                         132|                                                                                                         
                                                                                                                                          134

Chain C from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2zuqC01 C:1-119 Immunoglobulins                                                                                    2zuqC02 C:121-221 Immunoglobulins                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...ee...eeeeeeeeee..hhhhh.eeeeee.....eeeeeee......ee........eeeeee....eeeeeeeee.....eeeeee............eeee.......eeeee..........eeeeeeeeeee.....eeee........eee.........eeeeeeeeee.........eeeeee....eeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2zuq C   1 EVQLVESGGGLVKPGGSLKLSCAASGFAFSSYDMSWVRQTPEKRLEWVAYISSGGGSTYYPDTVKGRFTISRDNAKNTLYLQMSSLKSEDTAMYYCARPDAMDYWGQGTSVTVSSKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRGP 221
                                    10        20        30        40        50        60        70        80        90       100|      114    || 125       135       145       155       165       175       185       195       205       215      
                                                                                                                             100|           119|                                                                                                    
                                                                                                                              105            121

Chain D from PDB  Type:PROTEIN  Length:148
 aligned with DSBB_ECOLI | P0A6M2 from UniProtKB/Swiss-Prot  Length:176

    Alignment length:153
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159   
           DSBB_ECOLI    10 QGRGAWLLMAFTALALELTALWFQHVMLLKPCVLCIYERCALFGVLGAALIGAIAPKTPLRYVAMVIWLYSAFRGVQLTYEHTMLQLYPSPFATCDFMVRFPEWLPLDKWVPQVFVASGDCAERQWDFLGLEMPQWLLGIFIAYLIVAVLVVI 162
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) DsbB-2zuqD01 D:10-162                                                                                                                                     Pfam domains (1)
           Pfam domains (2) DsbB-2zuqD02 D:10-162                                                                                                                                     Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhh.hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........-----......................hhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zuq D  10 QGRGAWLLMAFTALALELTALWFQHVMLLKPSVLCIYERVALFGVLGAALIGAIAPKTPLRYVAMVIWLYSAFRGVQLTYEHTMLQLYPSPFATCDFMV-----LPLDKWVPQVFVASGDCAERQWDFLGLEMPQWLLGIFIAYLIVAVLVVI 162
                                    19        29        39        49        59        69        79        89        99        |-    |  119       129       139       149       159   
                                                                                                                            108   114

Chain E from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------2zuqE02 E:134-236 Immunoglobulins                                                                      --- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..........eee.eeee.............eeeeee......eeee.........................eee..hhhhh.eeeeee.....ee...ee.........eeeee..hhhhhhh.eeeeeeeeeee.........ee........eeeee.........eeeeeeeeeehhhhh...eeeeee........eeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zuq E  21 DIVMSQSPSSLAVSAGEKVTMSCKSSQSLLNSRTRKNYLAWYQQKPGQSPKLLIYWASTRESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYCKQSYNLYTFGGGTKLEIKADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 239
                                    30        40        50        60        70        80        90       100       110       120       130 ||    141       151       161       171       181       191       201       211       221       231        
                                                                                                                                         132|                                                                                                         
                                                                                                                                          134

Chain F from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2zuqF01 F:1-119 Immunoglobulins                                                                                        2zuqF02 F:121-215 Immunoglobulins                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...ee.....eeeeeee...hhhhh.eeeeee.....eeeeeee......ee........eeeeee....eeeeee...hhhhh.eeeeeee......eeee......ee.......eeeee..........eeeeeeeeeee.....eeee.hhh....eee.........eeeeeeeeee..........eeeee....eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zuq F   1 EVQLVESGGGLVKPGGSLKLSCAASGFAFSSYDMSWVRQTPEKRLEWVAYISSGGGSTYYPDTVKGRFTISRDNAKNTLYLQMSSLKSEDTAMYYCARPDYRSYAMDYWGQGTSVTVSSKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKK 215
                                    10        20        30        40        50        60        70        80        90       100       110       121       131       141       151       161       171       181       191       201       211    
                                                                                                                                                119|                                                                                              
                                                                                                                                                 121

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 2ZUQ)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Escherichia coli. Organism_taxid: 83333. Strain: k12. (1)

1a	2zuqB02	B:134-236
1b	2zuqE02	E:134-236
1c	2zuqC02	C:121-221
1d	2zuqF02	F:121-215
1e	2zuqC01	C:1-119
1f	2zuqF01	F:1-119

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: DsbB] (4)

Family: DsbB (4)

Escherichia coli (strain K12) (4)

1a	DsbB-2zuqD01	D:10-162
1b	DsbB-2zuqD02	D:10-162

Asymmetric Unit(hide GO term definitions)

Chain A,D (DSBB_ECOLI | P0A6M2)

molecular function
	GO:0009055	electron carrier activity	Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
	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.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0015035	protein disulfide oxidoreductase activity	Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds.
biological process
	GO:0022900	electron transport chain	A process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
	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.
	GO:0009408	response to heat	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism.
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric Unit
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	Sites
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	Cis Peptide Bonds
		Arg E:53 - Thr E:54	[ RasMol ]
		Glu C:154 - Pro C:155	[ RasMol ]
		Glu F:154 - Pro F:155	[ RasMol ]
		Leu A:37 - Leu A:38	[ RasMol ]
		Leu D:37 - Leu D:38	[ RasMol ]
		Phe C:152 - Pro C:153	[ RasMol ]
		Phe F:152 - Pro F:153	[ RasMol ]
		Pro A:65 - Lys A:66	[ RasMol ]
		Pro D:65 - Lys D:66	[ RasMol ]
		Ser B:27 - Pro B:28	[ RasMol ]
		Ser E:27 - Pro E:28	[ RasMol ]
		Tyr B:165 - Pro B:166	[ RasMol ]
		Tyr E:165 - Pro E:166	[ RasMol ]

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Access by PDB/NDB ID
	2zuq
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	DSBB_ECOLI \| P0A6M2
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	1.8.5.-
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UniProtKB/Swiss-Prot
	DSBB_ECOLI \| P0A6M2	:	2hi7 2k73 2k74 2leg 2ltq 2zup 3e9j

2hi7	THE SAME PROTEIN COMPLEXED WITH DSBA
2zup	THE SAME PROTEIN COMPLEXED WITH DSBA

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (12, 12)

Cis Peptide Bonds (13, 13)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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