2AQR - 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)

Title :   CU/ZN SUPEROXIDE DISMUTASE FROM NEISSERIA MENINGITIDIS K91Q MUTANT

Authors :   M. Didonato, C. J. Kassmann, C. K. Bruns, D. E. Cabelli, Z. Cao, L. B. Tabatabai, J. S. Kroll, E. D. Getzoff

Date :   18 Aug 05 (Deposition) - 31 Oct 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

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

Keywords :   Cu/Zn Superoxide Dismutase, Electrostatic Guidance, Neisseria Meningitidis, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Didonato, C. J. Kassmann, C. K. Bruns, D. E. Cabelli, Z. Cao, L. B. Tabatabai, J. S. Kroll, E. D. Getzoff
Cu/Zn Superoxide Dismutase From Neisseria Meningitidis K91Q Mutant
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - SUPEROXIDE DISMUTASE [CU-ZN]
	Chains	:	A, B, C
	EC Number	:	1.15.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	SODC
	Mutation	:	YES
	Organism Scientific	:	NEISSERIA MENINGITIDIS
	Organism Taxid	:	487

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 8)

No.	Name	Count	Type	Full Name
2	CU	2	Ligand/Ion	COPPER (II) ION
1	CU1	3	Ligand/Ion	COPPER (I) ION
3	ZN	3	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
2	CU	-1	Ligand/Ion	COPPER (II) ION
1	CU1	2	Ligand/Ion	COPPER (I) ION
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
2	CU	-1	Ligand/Ion	COPPER (II) ION
1	CU1	2	Ligand/Ion	COPPER (I) ION
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (1, 6)

No.	Name	Count	Type	Full Name
2	CU	-1	Ligand/Ion	COPPER (II) ION
1	CU1	6	Ligand/Ion	COPPER (I) ION
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:79 , HIS A:81 , HIS A:104 , HIS A:160	BINDING SITE FOR RESIDUE CU1 A 200
2	AC2	SOFTWARE	HIS B:79 , HIS B:81 , HIS B:104 , HIS B:160	BINDING SITE FOR RESIDUE CU1 B 200
3	AC3	SOFTWARE	HIS C:79 , HIS C:81 , HIS C:104 , HIS C:160	BINDING SITE FOR RESIDUE CU1 C 200
4	AC4	SOFTWARE	GLU A:73 , HIS A:133 , GLU B:73 , HIS B:133	BINDING SITE FOR RESIDUE CU A 250
5	AC5	SOFTWARE	GLU C:73 , HIS C:133	BINDING SITE FOR RESIDUE CU C 251
6	AC6	SOFTWARE	HIS A:104 , HIS A:113 , HIS A:122 , ASP A:125	BINDING SITE FOR RESIDUE ZN A 201
7	AC7	SOFTWARE	HIS B:104 , HIS B:113 , HIS B:122 , ASP B:125	BINDING SITE FOR RESIDUE ZN B 201
8	AC8	SOFTWARE	HIS C:104 , HIS C:113 , HIS C:122 , ASP C:125	BINDING SITE FOR RESIDUE ZN C 201

Asymmetric Unit

No.	Residues
1	A:86	-	A:182
2	B:86	-	B:182
3	C:86	-	C:182

Asymmetric Unit

No.	Residues
1	His A:169	-	Pro A:170
2	His B:169	-	Pro B:170
3	His C:169	-	Pro C:170

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

Asymmetric Unit (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SOD_CU_ZN_1	PS00087	Copper/Zinc superoxide dismutase signature 1.	SODC_NEIMB	77-87	3	A:77-87 B:77-87 C:77-87
2	SOD_CU_ZN_2	PS00332	Copper/Zinc superoxide dismutase signature 2.	SODC_NEIMB	174-185	3	A:174-185 B:174-185 C:174-185

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SOD_CU_ZN_1	PS00087	Copper/Zinc superoxide dismutase signature 1.	SODC_NEIMB	77-87	2	A:77-87 B:77-87 -
2	SOD_CU_ZN_2	PS00332	Copper/Zinc superoxide dismutase signature 2.	SODC_NEIMB	174-185	2	A:174-185 B:174-185 -

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SOD_CU_ZN_1	PS00087	Copper/Zinc superoxide dismutase signature 1.	SODC_NEIMB	77-87	2	- - C:77-87
2	SOD_CU_ZN_2	PS00332	Copper/Zinc superoxide dismutase signature 2.	SODC_NEIMB	174-185	2	- - C:174-185

Biological Unit 3 (2, 12)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SOD_CU_ZN_1	PS00087	Copper/Zinc superoxide dismutase signature 1.	SODC_NEIMB	77-87	6	A:77-87 B:77-87 C:77-87
2	SOD_CU_ZN_2	PS00332	Copper/Zinc superoxide dismutase signature 2.	SODC_NEIMB	174-185	6	A:174-185 B:174-185 C:174-185

(no "Exon" information available for 2AQR)

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:155
 aligned with SODC_NEIMB | Q59623 from UniProtKB/Swiss-Prot  Length:186

    Alignment length:155
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181     
           SODC_NEIMB    32 ASIEVKVQQLDPVNGNKDVGTVTITESNYGLVFTPDLQGLSEGLHGFHIHENPSCEPKEKEGKLTAGLGAGGHWDPKGAKQHGYPWQDDAHLGDLPALTVLHDGTATNPVLAPRLKHLDDVRGHSIMIHTGGDNHSDHPAPLGGGGPRMACGVIK 186
               SCOP domains d2aqra_ A: Cu,Zn superoxide dismutase, SOD                                                                                                                  SCOP domains
               CATH domains 2aqrA00 A:32-186  [code=2.60.40.200, no name defined]                                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.......eeeeeeeeeee..eeeeeeee.....eee.eeee.......ee....ee.hhhhh..........................eee.........eee....hhhhhh.eeeeee..........hhhhhh..eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------SOD_CU_ZN_1--------------------------------------------------------------------------------------SOD_CU_ZN_2 - PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2aqr A  32 ASIEVKVQQLDPVNGNKDVGTVTITESNYGLVFTPDLQGLSEGLHGFHIHENPSCEPKEQEGKLTAGLGAGGHWDPKGAKQHGYPWQDDAHLGDLPALTVLHDGTATNPVLAPRLKHLDDVRGHSIMIHTGGDNHSDHPAPLGGGGPRMACGVIK 186
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181

Chain B from PDB  Type:PROTEIN  Length:155
 aligned with SODC_NEIMB | Q59623 from UniProtKB/Swiss-Prot  Length:186

    Alignment length:155
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181     
           SODC_NEIMB    32 ASIEVKVQQLDPVNGNKDVGTVTITESNYGLVFTPDLQGLSEGLHGFHIHENPSCEPKEKEGKLTAGLGAGGHWDPKGAKQHGYPWQDDAHLGDLPALTVLHDGTATNPVLAPRLKHLDDVRGHSIMIHTGGDNHSDHPAPLGGGGPRMACGVIK 186
               SCOP domains d2aqrb_ B: Cu,Zn superoxide dismutase, SOD                                                                                                                  SCOP domains
               CATH domains 2aqrB00 B:32-186  [code=2.60.40.200, no name defined]                                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.......eeeeeeeeeee..eeeeeeee.....eee.eeee.......eee..eee.hhhhh..........................eee.........eee....hhhhhh.eeeeee..........hhhhhh..eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------SOD_CU_ZN_1--------------------------------------------------------------------------------------SOD_CU_ZN_2 - PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2aqr B  32 ASIEVKVQQLDPVNGNKDVGTVTITESNYGLVFTPDLQGLSEGLHGFHIHENPSCEPKEQEGKLTAGLGAGGHWDPKGAKQHGYPWQDDAHLGDLPALTVLHDGTATNPVLAPRLKHLDDVRGHSIMIHTGGDNHSDHPAPLGGGGPRMACGVIK 186
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181

Chain C from PDB  Type:PROTEIN  Length:155
 aligned with SODC_NEIMB | Q59623 from UniProtKB/Swiss-Prot  Length:186

    Alignment length:155
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181     
           SODC_NEIMB    32 ASIEVKVQQLDPVNGNKDVGTVTITESNYGLVFTPDLQGLSEGLHGFHIHENPSCEPKEKEGKLTAGLGAGGHWDPKGAKQHGYPWQDDAHLGDLPALTVLHDGTATNPVLAPRLKHLDDVRGHSIMIHTGGDNHSDHPAPLGGGGPRMACGVIK 186
               SCOP domains d2aqrc_ C: Cu,Zn superoxide dismutase, SOD                                                                                                                  SCOP domains
               CATH domains 2aqrC00 C:32-186  [code=2.60.40.200, no name defined]                                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.......eeeeeeeeeee..eeeeeeee.....eee.eeee.......eee..eee.hhhhh..........................eee.........eee....hhhhhh.eeeeee..........hhhhhh..eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------SOD_CU_ZN_1--------------------------------------------------------------------------------------SOD_CU_ZN_2 - PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2aqr C  32 ASIEVKVQQLDPVNGNKDVGTVTITESNYGLVFTPDLQGLSEGLHGFHIHENPSCEPKEQEGKLTAGLGAGGHWDPKGAKQHGYPWQDDAHLGDLPALTVLHDGTATNPVLAPRLKHLDDVRGHSIMIHTGGDNHSDHPAPLGGGGPRMACGVIK 186
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181

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(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

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Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Cu,Zn superoxide dismutase-like (165)

Family: Cu,Zn superoxide dismutase-like (158)

Protein domain: Cu,Zn superoxide dismutase, SOD (134)

Neisseria meningitidis [TaxId: 487] (6)

1a	d2aqra_	A:
1b	d2aqrc_	C:
1c	d2aqrb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: [code=2.60.40.200, no name defined] (125)

Neisseria meningitidis. Organism_taxid: 487. (6)

1a	2aqrA00	A:32-186
1b	2aqrB00	B:32-186
1c	2aqrC00	C:32-186

(no "Pfam Domain" information available for 2AQR)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (SODC_NEIMB | Q59623)

molecular function
	GO:0016209	antioxidant activity	Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0004784	superoxide dismutase activity	Catalysis of the reaction: 2 superoxide + 2 H+ = O2 + hydrogen peroxide.
biological process
	GO:0098869	cellular oxidant detoxification	Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
	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:0019430	removal of superoxide radicals	Any process, acting at the cellular level, involved in removing superoxide radicals (O2-) from a cell or organism, e.g. by conversion to dioxygen (O2) and hydrogen peroxide (H2O2).
	GO:0006801	superoxide metabolic process	The chemical reactions and pathways involving superoxide, the superoxide anion O2- (superoxide free radical), or any compound containing this species.
cellular component
	GO:0042597	periplasmic space	The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		CU	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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	Cis Peptide Bonds
		His A:169 - Pro A:170	[ RasMol ]
		His B:169 - Pro B:170	[ RasMol ]
		His C:169 - Pro C:170	[ RasMol ]

Biological Units
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Access by PDB/NDB ID
	2aqr
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	SODC_NEIMB \| Q59623
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	1.15.1.1
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	SODC_NEIMB \| Q59623	:	2aqn 2aqp 2aqq 2aqs 2aqt

Description

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Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (3, 3)

Cis Peptide Bonds (3, 3)

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SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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