3PZA - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   FULLY REDUCED (ALL-FERROUS) PYROCOCCUS RUBRERYTHRIN AFTER A 10 SECOND EXPOSURE TO PEROXIDE.

Authors :   B. D. Dillard, J. M. Demick, M. W. Adams, W. N. Lanzilotta

Date :   14 Dec 10 (Deposition) - 22 Jun 11 (Release) - 10 Aug 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

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

Keywords :   Rubrerythrin, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. D. Dillard, J. M. Demick, M. W. Adams, W. N. Lanzilotta
A Cryo-Crystallographic Time Course For Peroxide Reduction By Rubrerythrin From Pyrococcus Furiosus.
J. Biol. Inorg. Chem. V. 16 949 2011
PubMed-ID: 21647777 | Reference-DOI: 10.1007/S00775-011-0795-6

Molecule 1 - RUBRERYTHRIN
	Chains	:	A, B
	Organism Scientific	:	PYROCOCCUS FURIOSUS
	Organism Taxid	:	2261

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	FE2	6	Ligand/Ion	FE (II) ION
2	PEO	2	Ligand/Ion	HYDROGEN PEROXIDE

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	FE2	6	Ligand/Ion	FE (II) ION
2	PEO	2	Ligand/Ion	HYDROGEN PEROXIDE

Biological Unit 2 (2, 16)

No.	Name	Count	Type	Full Name
1	FE2	12	Ligand/Ion	FE (II) ION
2	PEO	4	Ligand/Ion	HYDROGEN PEROXIDE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:80 , GLU A:83 , GLU A:114 , FE2 A:173 , GLU B:19 , GLU B:52 , FE2 B:174	BINDING SITE FOR RESIDUE PEO A 172
2	AC2	SOFTWARE	CYS A:142 , CYS A:145 , CYS A:157 , CYS A:160	BINDING SITE FOR RESIDUE FE2 A 1
3	AC3	SOFTWARE	GLU A:80 , GLU A:114 , HIS A:117 , PEO A:172 , GLU B:52	BINDING SITE FOR RESIDUE FE2 A 173
4	AC4	SOFTWARE	GLU A:19 , GLU A:52 , HIS A:55 , PEO B:1 , GLU B:114	BINDING SITE FOR RESIDUE FE2 A 174
5	AC5	SOFTWARE	GLU A:19 , GLU A:52 , FE2 A:174 , GLU B:80 , GLU B:83 , GLU B:114 , FE2 B:173	BINDING SITE FOR RESIDUE PEO B 1
6	AC6	SOFTWARE	CYS B:142 , CYS B:145 , CYS B:157 , CYS B:160	BINDING SITE FOR RESIDUE FE2 B 172
7	AC7	SOFTWARE	GLU A:52 , PEO B:1 , GLU B:80 , GLU B:114 , HIS B:117	BINDING SITE FOR RESIDUE FE2 B 173
8	AC8	SOFTWARE	GLU A:114 , PEO A:172 , GLU B:19 , GLU B:52 , HIS B:55	BINDING SITE FOR RESIDUE FE2 B 174

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

(no "Cis Peptide Bond" information available for 3PZA)

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

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

(no "Exon" information available for 3PZA)

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
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Chain A from PDB  Type:PROTEIN  Length:170
 aligned with Q9UWP7_9EURY | Q9UWP7 from UniProtKB/TrEMBL  Length:171

    Alignment length:170
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171
         Q9UWP7_9EURY     2 VVKRTMTKKFLEEAFAGESMAHMRYLIFAEKAEQEGFPNIAKLFRAIAYAEFVHAKNHFIALGKLGKTPENLQMGIEGETFEVEEMYPVYNKAAEFQGEKEAVRTTHYALEAEKIHAELYRKAKEKAEKGEDIEIKKVYICPICGYTAVDEAPEYCPVCGAPKEKFVVFE 171
               SCOP domains d3pzaa1 A:2-134 automated matches                                                                                                    d3pzaa2 A:135-171 automated matches   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eee......eee............hhhhheee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pza A   2 VVKRTMTKKFLEEAFAGESMAHMRYLIFAEKAEQEGFPNIAKLFRAIAYAEFVHAKNHFIALGKLGKTPENLQMGIEGETFEVEEMYPVYNKAAEFQGEKEAVRTTHYALEAEKIHAELYRKAKEKAEKGEDIEIKKVYICPICGYTAVDEAPEYCPVCGAPKEKFVVFE 171
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171

Chain B from PDB  Type:PROTEIN  Length:170
 aligned with Q9UWP7_9EURY | Q9UWP7 from UniProtKB/TrEMBL  Length:171

    Alignment length:170
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171
         Q9UWP7_9EURY     2 VVKRTMTKKFLEEAFAGESMAHMRYLIFAEKAEQEGFPNIAKLFRAIAYAEFVHAKNHFIALGKLGKTPENLQMGIEGETFEVEEMYPVYNKAAEFQGEKEAVRTTHYALEAEKIHAELYRKAKEKAEKGEDIEIKKVYICPICGYTAVDEAPEYCPVCGAPKEKFVVFE 171
               SCOP domains d3pzab1 B:2-134 automated matches                                                                                                    d3pzab2 B:135-171 automated matches   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------Rubrerythrin-3pzaB01 B:10-125                                                                                       ---------------------------------------------- Pfam domains (1)
           Pfam domains (2) --------Rubrerythrin-3pzaB02 B:10-125                                                                                       ---------------------------------------------- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eee......eee............hhhhheee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pza B   2 VVKRTMTKKFLEEAFAGESMAHMRYLIFAEKAEQEGFPNIAKLFRAIAYAEFVHAKNHFIALGKLGKTPENLQMGIEGETFEVEEMYPVYNKAAEFQGEKEAVRTTHYALEAEKIHAELYRKAKEKAEKGEDIEIKKVYICPICGYTAVDEAPEYCPVCGAPKEKFVVFE 171
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171

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: All alpha proteins (14657)

Fold: Ferritin-like (533)

Superfamily: Ferritin-like (489)

Family: Ferritin (232)

Protein domain: automated matches (70)

Pyrococcus furiosus [TaxId: 2261] (4)

1a	d3pzaa1	A:2-134
1b	d3pzab1	B:2-134

Class: Small proteins (3458)

Fold: Rubredoxin-like (572)

Superfamily: Rubredoxin-like (127)

Family: automated matches (7)

Protein domain: automated matches (7)

Pyrococcus furiosus [TaxId: 2261] (4)

2a	d3pzaa2	A:135-171
2b	d3pzab2	B:135-171

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ferritin (185)

Family: Rubrerythrin (18)

Pyrococcus furiosus (5)

1a	Rubrerythrin-3pzaB01	B:10-125
1b	Rubrerythrin-3pzaB02	B:10-125

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q9UWP7_9EURY | Q9UWP7)

molecular function
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	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.
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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Biological Units
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(no "Related Entries Specified in the PDB File" available for 3PZA)

Description

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Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

SS Bonds (0, 0)

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