2PD1 - JenaLib

Asym.Unit - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Biological Unit 5 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF NE2512 PROTEIN OF UNKNOWN FUNCTION FROM NITROSOMONAS EUROPAEA

Authors :   J. Osipiuk, E. Evdokimova, O. Kagan, A. Savchenko, A. Edwards, A. Joach Midwest Center For Structural Genomics (Mcsg)

Date :   30 Mar 07 (Deposition) - 01 May 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.86

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,C  (1x)
Biol. Unit 2: B,D  (1x)
Biol. Unit 3: A (2x),B (2x),C (2x),D (2x)
Biol. Unit 4: A,B,C,D  (1x)
Biol. Unit 5: A (1x),B (1x),C (1x),D (1x)

Keywords :   Unknown Function, Ne2512 Protein, Structural Genomics, Apc7253, Psi- 2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Osipiuk, E. Evdokimova, O. Kagan, A. Savchenko, A. Edwards, A. Joachimiak
Crystal Structure Of Ne2512 Protein Of Unknown Function Fro Nitrosomonas Europaea.
To Be Published
PubMed: search

Molecule 1 - HYPOTHETICAL PROTEIN
	Atcc	:	19718
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	NE2512
	Organism Scientific	:	NITROSOMONAS EUROPAEA
	Organism Taxid	:	915
	Strain	:	IFO 14298

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 11)

No.	Name	Count	Type	Full Name
1	ACT	3	Ligand/Ion	ACETATE ION
2	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (2, 5)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 3 (2, 12)

No.	Name	Count	Type	Full Name
1	ACT	4	Ligand/Ion	ACETATE ION
2	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 4 (2, 11)

No.	Name	Count	Type	Full Name
1	ACT	3	Ligand/Ion	ACETATE ION
2	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 5 (2, 6)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:40 , VAL A:52 , ASP A:54 , HIS A:65 , ILE A:70	BINDING SITE FOR RESIDUE ACT A 501
2	AC2	SOFTWARE	TRP B:40 , VAL B:52 , HIS B:65 , ILE B:70 , HOH B:594	BINDING SITE FOR RESIDUE ACT B 502
3	AC3	SOFTWARE	TRP C:40 , VAL C:52 , ASP C:54 , HIS C:65	BINDING SITE FOR RESIDUE ACT C 503

(no "SS Bond" information available for 2PD1)

(no "Cis Peptide Bond" information available for 2PD1)

(no "SAP(SNP)/Variant" information available for 2PD1)

(no "PROSITE Motif" information available for 2PD1)

(no "Exon" information available for 2PD1)

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:103
 aligned with Q82S47_NITEU | Q82S47 from UniProtKB/TrEMBL  Length:100

    Alignment length:103
                              1                                                                                                100 
                              |      8        18        28        38        48        58        68        78        88        98 | 
         Q82S47_NITEU     - --MTKLALFVRLEAKPGQEAALADFLASALPLANAESGTTAWFALKFGPSTFGVFDAFADEAGRQAHLNGQIAAALMANAATLLSSPPNIEKVELLAAKLPA-   -
               SCOP domains --d2pd1a1 A:1-100 Hypothetical protein NE2512                                                         - SCOP domains
               CATH domains 2pd1A01 A:-1-93  [code=3.30.70.900, no name defined]                                           -------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeee....hhhhhhhhhhhhhhhhhh...eeeeeeee....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 2pd1 A  -1 GHmTKLALFVRLEAKPGQEAALADFLASALPLANAESGTTAWFALKFGPSTFGVFDAFADEAGRQAHLNGQIAAALmANAATLLSSPPNIEKVELLAAKLPAG 101
                              |      8        18        28        38        48        58        68      | 78        88        98   
                              |                                                                        75-MSE                      
                              1-MSE

Chain B from PDB  Type:PROTEIN  Length:100
 aligned with Q82S47_NITEU | Q82S47 from UniProtKB/TrEMBL  Length:100

    Alignment length:100
                                    10        20        30        40        50        60        70        80        90       100
         Q82S47_NITEU     1 MTKLALFVRLEAKPGQEAALADFLASALPLANAESGTTAWFALKFGPSTFGVFDAFADEAGRQAHLNGQIAAALMANAATLLSSPPNIEKVELLAAKLPA 100
               SCOP domains d2pd1b_ B: Hypothetical protein NE2512                                                               SCOP domains
               CATH domains -2pd1B01 B:2-93  [code=3.30.70.900, no name defined]                                         ------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee....hhhhhhhhhhhhhhhhhh...eeeeeeee....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 2pd1 B   1 mTKLALFVRLEAKPGQEAALADFLASALPLANAESGTTAWFALKFGPSTFGVFDAFADEAGRQAHLNGQIAAALmANAATLLSSPPNIEKVELLAAKLPA 100
                            |       10        20        30        40        50        60        70    |   80        90       100
                            1-MSE                                                                    75-MSE

Chain C from PDB  Type:PROTEIN  Length:101
 aligned with Q82S47_NITEU | Q82S47 from UniProtKB/TrEMBL  Length:100

    Alignment length:101
                                                                                                                             100 
                                    10        20        30        40        50        60        70        80        90       100 
         Q82S47_NITEU     1 MTKLALFVRLEAKPGQEAALADFLASALPLANAESGTTAWFALKFGPSTFGVFDAFADEAGRQAHLNGQIAAALMANAATLLSSPPNIEKVELLAAKLPA-   -
               SCOP domains d2pd1c_ C: Hypothetical protein NE2512                                                                SCOP domains
               CATH domains -2pd1C01 C:2-93  [code=3.30.70.900, no name defined]                                         -------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee....hhhhhhhhhhhhhhhhhhh..eeeeeeeeee..eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 2pd1 C   1 mTKLALFVRLEAKPGQEAALADFLASALPLANAESGTTAWFALKFGPSTFGVFDAFADEAGRQAHLNGQIAAALmANAATLLSSPPNIEKVELLAAKLPAG 101
                            |       10        20        30        40        50        60        70    |   80        90       100 
                            1-MSE                                                                    75-MSE

Chain D from PDB  Type:PROTEIN  Length:101
 aligned with Q82S47_NITEU | Q82S47 from UniProtKB/TrEMBL  Length:100

    Alignment length:101
                                                                                                                             100 
                                    10        20        30        40        50        60        70        80        90       100 
         Q82S47_NITEU     1 MTKLALFVRLEAKPGQEAALADFLASALPLANAESGTTAWFALKFGPSTFGVFDAFADEAGRQAHLNGQIAAALMANAATLLSSPPNIEKVELLAAKLPA-   -
               SCOP domains d2pd1d_ D: Hypothetical protein NE2512                                                                SCOP domains
               CATH domains -2pd1D01 D:2-93  [code=3.30.70.900, no name defined]                                         -------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee....hhhhhhhhhhhhhhhhhh...eeeeeeeeee..eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 2pd1 D   1 mTKLALFVRLEAKPGQEAALADFLASALPLANAESGTTAWFALKFGPSTFGVFDAFADEAGRQAHLNGQIAAALmANAATLLSSPPNIEKVELLAAKLPAG 101
                            |       10        20        30        40        50        60        70    |   80        90       100 
                            1-MSE                                                                    75-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) (23004)

Fold: Ferredoxin-like (1795)

Superfamily: Dimeric alpha+beta barrel (122)

Family: PA3566-like (6)

Protein domain: Hypothetical protein NE2512 (1)

Nitrosomonas europaea [TaxId: 915] (1)

1a	d2pd1a1	A:1-100
1b	d2pd1b_	B:
1c	d2pd1c_	C:
1d	d2pd1d_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Alpha-Beta Plaits (1688)

Homologous Superfamily: [code=3.30.70.900, no name defined] (47)

Nitrosomonas europaea. Organism_taxid: 915. Strain: ifo 14298. (1)

1a	2pd1A01	A:-1-93
1b	2pd1B01	B:2-93
1c	2pd1C01	C:2-93
1d	2pd1D01	D:2-93

(no "Pfam Domain" information available for 2PD1)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 2PD1)

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
		ACT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2pd1)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]
		Biological Unit 4	[ Jena3D ]
		Biological Unit 5	[ 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 \| Biol. Unit 2 PNG format \| Biol. Unit 3 PNG format \| Biol. Unit 4 PNG format \| Biol. Unit 5 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
	2pd1
		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
	Q82S47_NITEU \| Q82S47
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

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
	Q82S47_NITEU \| Q82S47
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 2PD1)

(no "Related Entries Specified in the PDB File" available for 2PD1)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 11)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (1, 4)

Pfam Domains (0, 0)

Gene Ontology (0, 0)

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