2PLM - 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)

Title :   CRYSTAL STRUCTURE OF THE PROTEIN TM0936 FROM THERMOTOGA MARITIMA COMPLEXED WITH ZN AND S-INOSYLHOMOCYSTEINE

Authors :   A. A. Fedorov, E. V. Fedorov, J. C. Hermann, R. Marti-Arbona, B. K. Shoichet, F. M. Raushel, S. C. Almo

Date :   20 Apr 07 (Deposition) - 17 Jul 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Tm0936, Function Prediction, Amidohydrolase, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. C. Hermann, R. Marti-Arbona, A. A. Fedorov, E. Fedorov, S. C. Almo, B. K. Shoichet, F. M. Raushel
Structure-Based Activity Prediction For An Enzyme Of Unknown Function
Nature V. 448 775 2007
PubMed-ID: 17603473 | Reference-DOI: 10.1038/NATURE05981
(for further references see the PDB file header)

Molecule 1 - UNCHARACTERIZED PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 2)

No.	Name	Count	Type	Full Name
1	SIB	1	Ligand/Ion	(2S)-2-AMINO-4-({[(2S,3S,4R,5R)-3,4-DIHYDROXY-5-(6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)TETRAHYDROFURAN-2-YL]METHYL}THIO)BUTANOIC ACID
2	ZN	1	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	SIB	1	Ligand/Ion	(2S)-2-AMINO-4-({[(2S,3S,4R,5R)-3,4-DIHYDROXY-5-(6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)TETRAHYDROFURAN-2-YL]METHYL}THIO)BUTANOIC ACID
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	SIB	2	Ligand/Ion	(2S)-2-AMINO-4-({[(2S,3S,4R,5R)-3,4-DIHYDROXY-5-(6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)TETRAHYDROFURAN-2-YL]METHYL}THIO)BUTANOIC ACID
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:55 , HIS A:57 , HIS A:200 , ASP A:279 , HOH A:409	BINDING SITE FOR RESIDUE ZN A 407
2	AC2	SOFTWARE	HIS A:57 , MET A:60 , PHE A:72 , TRP A:75 , VAL A:80 , GLU A:84 , MET A:114 , ARG A:136 , GLY A:137 , ARG A:148 , HIS A:173 , HIS A:200 , GLU A:203 , SER A:253 , ASP A:279 , HOH A:409 , HOH A:432 , HOH A:442	BINDING SITE FOR RESIDUE SIB A 408

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

Asymmetric Unit

No.	Residues
1	Asn A:284	-	Asn A:285
2	Phe A:351	-	Pro A:352

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

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

(no "Exon" information available for 2PLM)

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:404
 aligned with MTAD_THEMA | Q9X034 from UniProtKB/Swiss-Prot  Length:406

    Alignment length:404
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400    
           MTAD_THEMA     1 MIIGNCLILKDFSSEPFWGAVEIENGTIKRVLQGEVKVDLDLSGKLVMPALFNTHTHAPMTLLRGVAEDLSFEEWLFSKVLPIEDRLTEKMAYYGTILAQMEMARHGIAGFVDMYFHEEWIAKAVRDFGMRALLTRGLVDSNGDDGGRLEENLKLYNEWNGFEGRIFVGFGPHSPYLCSEEYLKRVFDTAKSLNAPVTIHLYETSKEEYDLEDILNIGLKEVKTIAAHCVHLPERYFGVLKDIPFFVSHNPASNLKLGNGIAPVQRMIEHGMKVTLGTDGAASNNSLNLFFEMRLASLLQKAQNPRNLDVNTCLKMVTYDGAQAMGFKSGKIEEGWNADLVVIDLDLPEMFPVQNIKNHLVHAFSGEVFATMVAGKWIYFDGEYPTIDSEEVKRELARIEKELY 404
               SCOP domains d2plma1 A:1-49,A:331-404                         d2plma2 A:50-330 Hypothetical protein TM0936, probable catalytic domain                                                                                                                                                                                                                  d2plma1 A:1-49,A:331-404 Hypothetical protein TM0936                       SCOP domains
               CATH domains 2plmA01 A:1-49,A:331-384                         2plmA02 A:50-330 Metal-dependent hydrolases                                                                                                                                                                                                                                              2plmA01 A:1-49,A:331-384 Urease, subunit C, domain 1  -------------------- CATH domains
               Pfam domains ---------------------------------------------Amidohydro_1-2plmA01 A:46-344                                                                                                                                                                                                                                                                              ------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee........eeeeeeee..eeeeeee......ee...eeeee.eeeeeehhhhhhhh......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhhhhhh.eeeeeeee........hhhhhhhhhhhhhhhhhh.eeeeeee......hhhhhhhhhhhhhhhh..eeeee.........hhhhhh.......eeeee....hhhhhhhhh...eeeeehhhhhhhh.....hhhhhhhh..eeee...........hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.............eeeee..hhhhhhhhhhhhhhhhh......eeee..eeeee.......hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2plm A   1 MIIGNCLILKDFSSEPFWGAVEIENGTIKRVLQGEVKVDLDLSGKLVMPALFNTHTHAPMTLLRGVAEDLSFEEWLFSKVLPIEDRLTEKMAYYGTILAQMEMARHGIAGFVDMYFHEEWIAKAVRDFGMRALLTRGLVDSNGDDGGRLEENLKLYNEWNGFEGRIFVGFGPHSPYLCSEEYLKRVFDTAKSLNAPVTIHLYETSKEEYDLEDILNIGLKEVKTIAAHCVHLPERYFGVLKDIPFFVSHNPASNLKLGNGIAPVQRMIEHGMKVTLGTDGAASNNSLNLFFEMRLASLLQKAQNPRNLDVNTCLKMVTYDGAQAMGFKSGKIEEGWNADLVVIDLDLPEMFPVQNIKNHLVHAFSGEVFATMVAGKWIYFDGEYPTIDSEEVKRELARIEKELY 404
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Metal-dependent hydrolases (190)

Thermotoga maritima. Organism_taxid: 2336. (1)

2plmA02

A:50-330

Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: Urease, subunit C; domain 1 (95)

Homologous Superfamily: Urease, subunit C, domain 1 (95)

Thermotoga maritima. Organism_taxid: 2336. (1)

2plmA01

A:1-49,A:331-384

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Amidohydrolase (126)

Family: Amidohydro_1 (28)

Thermotoga maritima (2)

Amidohydro_1-2plmA01

A:46-344

Asymmetric Unit(hide GO term definitions)

Chain A (MTAD_THEMA | Q9X034)

molecular function
	GO:0090614	5'-methylthioadenosine deaminase activity	Catalysis of the reaction: 5'methyl thioadenosine + H2O = 5'methyl thioinosine + NH3.
	GO:0050270	S-adenosylhomocysteine deaminase activity	Catalysis of the reaction: S-adenosyl-L-homocysteine + H(2)O + H(+) = S-inosyl-L-homocysteine + NH(4)(+).
	GO:0004000	adenosine deaminase activity	Catalysis of the reaction: adenosine + H2O = inosine + NH3.
	GO:0019239	deaminase activity	Catalysis of the removal of an amino group from a substrate, producing ammonia (NH3).
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0016810	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0019700	organic phosphonate catabolic process	The chemical reactions and pathways resulting in the breakdown of phosphonates, any organic compound containing one or more C-PO(OH)2 or C-PO(OR)2 (with R=alkyl, aryl) groups. Catabolism of phosphonic acid itself, an inorganic compound without the biochemically relevant C-P bond, is not included.

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
		SIB	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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

	Cis Peptide Bonds
		Asn A:284 - Asn A:285	[ RasMol ]
		Phe A:351 - Pro A:352	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ 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 ](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
	2plm
		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
	MTAD_THEMA \| Q9X034
		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
	MTAD_THEMA \| Q9X034
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	MTAD_THEMA \| Q9X034	:	1j6p 1p1m

1j6p	THE SAME PROTEIN, APO FORM
1p1m	THE SAME PROTEIN COMPLEXED WITH NI AND METHIONINE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (2, 2)

Pfam Domains (1, 1)

Gene Ontology (8, 8)

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