1NM3 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HEAMOPHILUS INFLUENZA HYBRID-PRX5

Authors :   S. J. Kim, J. R. Woo, Y. S. Hwang, D. G. Jeong, D. H. Shin, K. H. Kim, S. E. Ryu

Date :   08 Jan 03 (Deposition) - 25 Mar 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Hybrid, Peroxiredoxin, Glutaredoxin, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. J. Kim, J. R. Woo, Y. S. Hwang, D. G. Jeong, D. H. Shin, K. Kim, S. E. Ryu
The Tetrameric Structure Of Haemophilus Influenza Hybrid Prx5 Reveals Interactions Between Electron Donor And Acceptor Proteins.
J. Biol. Chem. V. 278 10790 2003
PubMed-ID: 12529327 | Reference-DOI: 10.1074/JBC.M209553200

Molecule 1 - PROTEIN HI0572
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET17B
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	HAEMOPHILUS INFLUENZAE
	Organism Taxid	:	727
	Synonym	:	HYBRID PEROXIREDOXIN

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 18)

No.	Name	Count	Type	Full Name
1	MSE	14	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 36)

No.	Name	Count	Type	Full Name
1	MSE	28	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	8	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:21 , VAL A:113 , GLY A:114 , LYS A:122	BINDING SITE FOR RESIDUE SO4 A 501
2	AC2	SOFTWARE	ARG A:17 , ASN A:144 , PRO B:47	BINDING SITE FOR RESIDUE SO4 A 502
3	AC3	SOFTWARE	ASP B:20 , PRO B:178 , GLY B:179	BINDING SITE FOR RESIDUE SO4 B 503
4	AC4	SOFTWARE	ASP A:24 , THR A:26 , ASP A:117 , ARG B:15	BINDING SITE FOR RESIDUE SO4 A 504

Asymmetric Unit

No.	Residues
1	A:180	-	A:183
2	B:180	-	B:183

Asymmetric Unit

No.	Residues
1	Val A:220	-	Pro A:221
2	Val B:220	-	Pro B:221

(no "SAP(SNP)/Variant" information available for 1NM3)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLUTAREDOXIN_2	PS51354	Glutaredoxin domain profile.	PRX5_HAEIN	160-241	2	A:160-239 B:160-241
2	GLUTAREDOXIN_1	PS00195	Glutaredoxin active site.	PRX5_HAEIN	174-190	2	A:174-190 B:174-190

Biological Unit 1 (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLUTAREDOXIN_2	PS51354	Glutaredoxin domain profile.	PRX5_HAEIN	160-241	4	A:160-239 B:160-241
2	GLUTAREDOXIN_1	PS00195	Glutaredoxin active site.	PRX5_HAEIN	174-190	4	A:174-190 B:174-190

(no "Exon" information available for 1NM3)

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:237
 aligned with PRX5_HAEIN | P44758 from UniProtKB/Swiss-Prot  Length:241

    Alignment length:237
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       
           PRX5_HAEIN     3 SMEGKKVPQVTFRTRQGDKWVDVTTSELFDNKTVIVFSLPGAFTPTCSSSHLPRYNELAPVFKKYGVDDILVVSVNDTFVMNAWKEDEKSENISFIPDGNGEFTEGMGMLVGKEDLGFGKRSWRYSMLVKNGVVEKMFIEPNEPGDPFKVSDADTMLKYLAPQHQVQESISIFTKPGCPFCAKAKQLLHDKGLSFEEIILGHDATIVSVRAVSGRTTVPQVFIGGKHIGGSDDLEKY 239
               SCOP domains d1nm3a2 A:3-165 N-terminal, Prx domain of Hybrid-Prx5                                                                                                              d1nm3a1 A:166-239 C-terminal, Grx domain of Hybrid-Prx5                    SCOP domains
               CATH domains ---1nm3A01 A:6-164 Glutaredoxin                                                                                                                                   -----1nm3A02 A:170-239 Glutaredoxin                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeee..eeeeeehhhhhh..eeeeeee....hhhhhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhh.....eeee...hhhhhhh..eee.......eee..eeeeee..eeeeeee............hhhhhhhhhh........eeeee...hhhhhhhhhhhhhhh...eeee.....hhhhhhhhh......eeee..eeeehhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------GLUTAREDOXIN_2  PDB: A:160-239 UniProt: 160-241                                  PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------GLUTAREDOXIN_1   ------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nm3 A   3 SmEGKKVPQVTFRTRQGDKWVDVTTSELFDNKTVIVFSLPGAFTPTCSSSHLPRYNELAPVFKKYGVDDILVVSVNDTFVmNAWKEDEKSENISFIPDGNGEFTEGmGmLVGKEDLGFGKRSWRYSmLVKNGVVEKmFIEPNEPGDPFKVSDADTmLKYLAPQHQVQESISIFTKPGCPFCAKAKQLLHDKGLSFEEIILGHDATIVSVRAVSGRTTVPQVFIGGKHIGGSDDLEKY 239
                             |      12        22        32        42        52        62        72        82|       92       102      |112       122      |132      |142       152     | 162       172       182       192       202       212       222       232       
                             |                                                                             83-MSE                   109-MSE             129-MSE   139-MSE            158-MSE                                                                             
                             4-MSE                                                                                                    111-MSE

Chain B from PDB  Type:PROTEIN  Length:239
 aligned with PRX5_HAEIN | P44758 from UniProtKB/Swiss-Prot  Length:241

    Alignment length:239
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232         
           PRX5_HAEIN     3 SMEGKKVPQVTFRTRQGDKWVDVTTSELFDNKTVIVFSLPGAFTPTCSSSHLPRYNELAPVFKKYGVDDILVVSVNDTFVMNAWKEDEKSENISFIPDGNGEFTEGMGMLVGKEDLGFGKRSWRYSMLVKNGVVEKMFIEPNEPGDPFKVSDADTMLKYLAPQHQVQESISIFTKPGCPFCAKAKQLLHDKGLSFEEIILGHDATIVSVRAVSGRTTVPQVFIGGKHIGGSDDLEKYFA 241
               SCOP domains d1nm3b2 B:3-165 N-terminal, Prx domain of Hybrid-Prx5                                                                                                              d1nm3b1 B:166-241 C-terminal, Grx domain of Hybrid-Prx5                      SCOP domains
               CATH domains ---1nm3B01 B:6-164 Glutaredoxin                                                                                                                                   -----1nm3B02 B:170-237 Glutaredoxin                                      ---- CATH domains
           Pfam domains (1) -Redoxin-1nm3B03 B:4-159                                                                                                                                     ------------Glutaredoxin-1nm3B01 B:172-230                             ----------- Pfam domains (1)
           Pfam domains (2) -Redoxin-1nm3B04 B:4-159                                                                                                                                     ------------Glutaredoxin-1nm3B02 B:172-230                             ----------- Pfam domains (2)
         Sec.struct. author ..........eeeeee..eeeeeehhhhhh..eeeeeee..........hhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhh....eeee...hhhhhhh..eee.......eee..eeeeee..eeeeeee............hhhhhhhhhh........eeeee...hhhhhhhhhhhhh.....eeee.....hhhhhhhhhh.....eeee..eeeehhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------GLUTAREDOXIN_2  PDB: B:160-241 UniProt: 160-241                                    PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------GLUTAREDOXIN_1   --------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nm3 B   3 SmEGKKVPQVTFRTRQGDKWVDVTTSELFDNKTVIVFSLPGAFTPTCSSSHLPRYNELAPVFKKYGVDDILVVSVNDTFVmNAWKEDEKSENISFIPDGNGEFTEGmGmLVGKEDLGFGKRSWRYSmLVKNGVVEKmFIEPNEPGDPFKVSDADTmLKYLAPQHQVQESISIFTKPGCPFCAKAKQLLHDKGLSFEEIILGHDATIVSVRAVSGRTTVPQVFIGGKHIGGSDDLEKYFA 241
                             |      12        22        32        42        52        62        72        82|       92       102      |112       122      |132      |142       152     | 162       172       182       192       202       212       222       232         
                             4-MSE                                                                         83-MSE                   109-MSE             129-MSE   139-MSE            158-MSE                                                                               
                                                                                                                                      111-MSE

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: Thioredoxin fold (994)

Superfamily: Thioredoxin-like (992)

Family: Glutathione peroxidase-like (136)

Protein domain: N-terminal, Prx domain of Hybrid-Prx5 (1)

Haemophilus influenzae [TaxId: 727] (1)

1a	d1nm3a2	A:3-165
1b	d1nm3b2	B:3-165

Family: Thioltransferase (167)

Protein domain: C-terminal, Grx domain of Hybrid-Prx5 (1)

Haemophilus influenzae [TaxId: 727] (1)

2a	d1nm3a1	A:166-239
2b	d1nm3b1	B:166-241

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Glutaredoxin (620)

Homologous Superfamily: Glutaredoxin (617)

Haemophilus influenzae. Organism_taxid: 727. (1)

1a	1nm3A01	A:6-164
1b	1nm3B01	B:6-164
1c	1nm3A02	A:170-239
1d	1nm3B02	B:170-237

Asymmetric Unit(hide GO term definitions)

Chain A,B (PRX5_HAEIN | P44758)

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:0004601	peroxidase activity	Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O.
	GO:0051920	peroxiredoxin activity	Catalysis of the reaction: 2 R'-SH + ROOH = R'-S-S-R' + H2O + ROH.
	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:0045454	cell redox homeostasis	Any process that maintains the redox environment of a cell or compartment within a cell.
	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.
cellular component
	GO:0005623	cell	The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Val A:220 - Pro A:221	[ RasMol ]
		Val B:220 - Pro B:221	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1nm3
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	PRX5_HAEIN \| P44758
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	PRX5_HAEIN \| P44758
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 1NM3)

(no "Related Entries Specified in the PDB File" available for 1NM3)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 18)

Sites (4, 4)

SS Bonds (2, 2)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 4)

CATH Domains (1, 4)

Pfam Domains (2, 4)

Gene Ontology (9, 9)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File