2D16 - JenaLib

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)

Title :   CRYSTAL STRUCTURE OF PH1918 PROTEIN FROM PYROCOCCUS HORIKOSHII OT3

Authors :   N. K. Lokanath, N. Kunishima, Riken Structural Genomics/Proteomic Initiative (Rsgi)

Date :   14 Aug 05 (Deposition) - 31 Oct 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.65

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

Keywords :   Hypothetical, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. K. Lokanath, N. Kunishima
Crystal Structure Of Ph1918 Protein From Pyrococcus Horikoshii Ot3
To Be Published
PubMed: search

Molecule 1 - HYPOTHETICAL PROTEIN PH1918
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	BL21-CODONPLUS (DE3)-RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLAMID
	Organism Scientific	:	PYROCOCCUS HORIKOSHII
	Organism Taxid	:	70601
	Strain	:	OT3

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	GOL	4	Ligand/Ion	GLYCEROL
2	NA	4	Ligand/Ion	SODIUM ION

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	GOL	4	Ligand/Ion	GLYCEROL
2	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (1, 6)

No.	Name	Count	Type	Full Name
1	GOL	6	Ligand/Ion	GLYCEROL
2	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 3 (1, 6)

No.	Name	Count	Type	Full Name
1	GOL	6	Ligand/Ion	GLYCEROL
2	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:130 , HOH A:1009	BINDING SITE FOR RESIDUE NA A 1001
2	AC2	SOFTWARE	ILE B:130 , HOH B:1003	BINDING SITE FOR RESIDUE NA B 1002
3	AC3	SOFTWARE	ILE C:130 , HOH C:1005	BINDING SITE FOR RESIDUE NA C 1003
4	AC4	SOFTWARE	ILE D:130 , HOH D:1124	BINDING SITE FOR RESIDUE NA D 1004
5	AC5	SOFTWARE	LEU A:37 , VAL A:40 , PRO A:41 , GLY A:42 , HOH A:1021 , TYR B:159	BINDING SITE FOR RESIDUE GOL A 646
6	AC6	SOFTWARE	ILE A:157 , LEU B:37 , VAL B:40 , PRO B:41 , GLY B:42 , HOH B:1007	BINDING SITE FOR RESIDUE GOL B 647
7	AC7	SOFTWARE	LEU C:37 , VAL C:40 , PRO C:41 , GLY C:42 , HOH C:1019 , HOH C:1132 , TYR D:159	BINDING SITE FOR RESIDUE GOL C 648
8	AC8	SOFTWARE	TYR C:159 , LEU D:37 , VAL D:40 , PRO D:41 , GLY D:42 , HOH D:1011	BINDING SITE FOR RESIDUE GOL D 649

(no "SS Bond" information available for 2D16)

(no "Cis Peptide Bond" information available for 2D16)

(no "SAP(SNP)/Variant" information available for 2D16)

(no "PROSITE Motif" information available for 2D16)

(no "Exon" information available for 2D16)

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:162
 aligned with O59581_PYRHO | O59581 from UniProtKB/TrEMBL  Length:162

    Alignment length:162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  
         O59581_PYRHO     1 MVRIEVIDIEKPEGVEVIIGQGNFSIFTVDDLARALLTAVPGIKFGIAMNEAKPQLTRYTGNDPELEALAAKNAVKIGAGHVFVILMKNAYPINVLNTIKNHPAVAMIYGASENPFQVIVAETELGRAVIGVVDGKAANKIETDEQKKERRELVEKIGYKID 162
               SCOP domains d2d16a_ A: automated matches                                                                                                                                       SCOP domains
               CATH domains 2d16A00 A:1-162 hypothetical protein tt1634                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.......eeeeeee.hhhhhhhhhhhhhhhhh...eeeeeeee....eeeeee.hhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhh...eeeeeeee...eeeeeee....eeeeeeee........hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2d16 A   1 MVRIEVIDIEKPEGVEVIIGQGNFSIFTVDDLARALLTAVPGIKFGIAMNEAKPQLTRYTGNDPELEALAAKNAVKIGAGHVFVILMKNAYPINVLNTIKNHPAVAMIYGASENPFQVIVAETELGRAVIGVVDGKAANKIETDEQKKERRELVEKIGYKID 162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain B from PDB  Type:PROTEIN  Length:161
 aligned with O59581_PYRHO | O59581 from UniProtKB/TrEMBL  Length:162

    Alignment length:161
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161 
         O59581_PYRHO     2 VRIEVIDIEKPEGVEVIIGQGNFSIFTVDDLARALLTAVPGIKFGIAMNEAKPQLTRYTGNDPELEALAAKNAVKIGAGHVFVILMKNAYPINVLNTIKNHPAVAMIYGASENPFQVIVAETELGRAVIGVVDGKAANKIETDEQKKERRELVEKIGYKID 162
               SCOP domains d2d16b_ B: automated matches                                                                                                                                      SCOP domains
               CATH domains 2d16B00 B:2-162 hypothetical protein tt1634                                                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.......eeeeeee.hhhhhhhhhhhhhhhhh...eeeeeeee....eeeeee.hhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhh...eeeeeeee...eeeeeee....eeeeeeee........hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d16 B   2 VRIEVIDIEKPEGVEVIIGQGNFSIFTVDDLARALLTAVPGIKFGIAMNEAKPQLTRYTGNDPELEALAAKNAVKIGAGHVFVILMKNAYPINVLNTIKNHPAVAMIYGASENPFQVIVAETELGRAVIGVVDGKAANKIETDEQKKERRELVEKIGYKID 162
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

Chain C from PDB  Type:PROTEIN  Length:162
 aligned with O59581_PYRHO | O59581 from UniProtKB/TrEMBL  Length:162

    Alignment length:162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  
         O59581_PYRHO     1 MVRIEVIDIEKPEGVEVIIGQGNFSIFTVDDLARALLTAVPGIKFGIAMNEAKPQLTRYTGNDPELEALAAKNAVKIGAGHVFVILMKNAYPINVLNTIKNHPAVAMIYGASENPFQVIVAETELGRAVIGVVDGKAANKIETDEQKKERRELVEKIGYKID 162
               SCOP domains d2d16c_ C: automated matches                                                                                                                                       SCOP domains
               CATH domains 2d16C00 C:1-162 hypothetical protein tt1634                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.......eeeeeee.hhhhhhhhhhhhhhhhh...eeeeeeee....eeeeee.hhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhh...eeeeeeee...eeeeeee....eeeeeeee........hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2d16 C   1 MVRIEVIDIEKPEGVEVIIGQGNFSIFTVDDLARALLTAVPGIKFGIAMNEAKPQLTRYTGNDPELEALAAKNAVKIGAGHVFVILMKNAYPINVLNTIKNHPAVAMIYGASENPFQVIVAETELGRAVIGVVDGKAANKIETDEQKKERRELVEKIGYKID 162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain D from PDB  Type:PROTEIN  Length:161
 aligned with O59581_PYRHO | O59581 from UniProtKB/TrEMBL  Length:162

    Alignment length:161
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161 
         O59581_PYRHO     2 VRIEVIDIEKPEGVEVIIGQGNFSIFTVDDLARALLTAVPGIKFGIAMNEAKPQLTRYTGNDPELEALAAKNAVKIGAGHVFVILMKNAYPINVLNTIKNHPAVAMIYGASENPFQVIVAETELGRAVIGVVDGKAANKIETDEQKKERRELVEKIGYKID 162
               SCOP domains d2d16d_ D: automated matches                                                                                                                                      SCOP domains
               CATH domains 2d16D00 D:2-162 hypothetical protein tt1634                                                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.......eeeeeee.hhhhhhhhhhhhhhhhh...eeeeeeee....eeeeee.hhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhh...eeeeeeee...eeeeeee....eeeeeeee........hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d16 D   2 VRIEVIDIEKPEGVEVIIGQGNFSIFTVDDLARALLTAVPGIKFGIAMNEAKPQLTRYTGNDPELEALAAKNAVKIGAGHVFVILMKNAYPINVLNTIKNHPAVAMIYGASENPFQVIVAETELGRAVIGVVDGKAANKIETDEQKKERRELVEKIGYKID 162
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

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: Ta1353-like (7)

Superfamily: Ta1353-like (7)

Family: automated matches (5)

Protein domain: automated matches (5)

Pyrococcus horikoshii [TaxId: 70601] (1)

1a	d2d16a_	A:
1b	d2d16b_	B:
1c	d2d16c_	C:
1d	d2d16d_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: hypothetical protein tt1634 (7)

Homologous Superfamily: hypothetical protein tt1634 (7)

Pyrococcus horikoshii ot3. Organism_taxid: 70601. Strain: ot3. (1)

1a	2d16B00	B:2-162
1b	2d16D00	D:2-162
1c	2d16A00	A:1-162
1d	2d16C00	C:1-162

(no "Pfam Domain" information available for 2D16)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 2D16)

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
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2d16)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ 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 ](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
	2d16
		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
	O59581_PYRHO \| O59581
		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
	O59581_PYRHO \| O59581
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 2D16)

(no "Related Entries Specified in the PDB File" available for 2D16)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

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