4NDA - 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 3-NITRO-TYROSINE TRNA SYNTHETASE (5B) BOUND TO 3-NITRO-TYROSINE

Authors :   R. B. Cooley, C. M. Driggers, P. A. Karplus, R. A. Mehl

Date :   25 Oct 13 (Deposition) - 19 Mar 14 (Release) - 16 Apr 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Rosmann Fold, 3-Nitro-Tyrosine Amino-Acyl Trna Synthetase, Trna, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. B. Cooley, J. L. Feldman, C. M. Driggers, T. A. Bundy, A. L. Stokes, P. A. Karplus, R. A. Mehl
Structural Basis Of Improved Second-Generation 3-Nitro-Tyrosine Trna Synthetases.
Biochemistry V. 53 1916 2014
PubMed-ID: 24611875 | Reference-DOI: 10.1021/BI5001239

Molecule 1 - TYROSINE--TRNA LIGASE
	Chains	:	A
	EC Number	:	6.1.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PET28A
	Gene	:	MJ0389, TYRS, TYRS MJ0389
	Mutation	:	YES
	Organism Scientific	:	METHANOCALDOCOCCUS JANNASCHII
	Organism Taxid	:	243232
	Strain	:	ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
	Synonym	:	TYROSYL-TRNA SYNTHETASE, TYRRS

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 4)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	NA	1	Ligand/Ion	SODIUM ION
3	NIY	1	Ligand/Ion	META-NITRO-TYROSINE

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	GOL	4	Ligand/Ion	GLYCEROL
2	NA	-1	Ligand/Ion	SODIUM ION
3	NIY	2	Ligand/Ion	META-NITRO-TYROSINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:34 , PHE A:35 , GLU A:36 , LEU A:65 , ALA A:67 , CYS A:70 , GLN A:109 , TYR A:151 , GLN A:155 , SER A:158 , GLN A:173 , HOH A:1002 , HOH A:1034 , HOH A:1053 , HOH A:1059	BINDING SITE FOR RESIDUE NIY A 401
2	AC2	SOFTWARE	ARG A:223 , ASN A:289 , ALA A:292 , GLU A:293	BINDING SITE FOR RESIDUE GOL A 402
3	AC3	SOFTWARE	LEU A:136 , VAL A:195 , LYS A:204 , HOH A:1124 , HOH A:1250	BINDING SITE FOR RESIDUE GOL A 403
4	AC4	SOFTWARE	ASP A:27 , THR A:126 , LEU A:127 , LYS A:128 , PRO A:144 , HOH A:1064	BINDING SITE FOR RESIDUE NA A 404

(no "SS Bond" information available for 4NDA)

Asymmetric Unit

No.	Residues
1	Ile A:15	-	Ser A:16
2	Tyr A:251	-	Pro A:252

(no "SAP(SNP)/Variant" information available for 4NDA)

(no "PROSITE Motif" information available for 4NDA)

(no "Exon" information available for 4NDA)

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:308
                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d4ndaa_ A: automated matches                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh...eeehhhhhhhhhh....eeeeee......hhhhhhhhhhhhhhhhh..eeeeeehhhhhhhh...hhhhhhhhhhhhhhhhhhh....eeee.hhh..hhhhhhhhhhhhh..hhhhhhhhh..........hhhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhh....eeeee............hhhhh.......hhhhhhhhhhhh.........hhhhhhhhhh....eee..hhhhh..eee.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nda A   1 MDEFEMIKRNTSEIISEEELREVLKKDEKSAHIGFEPSGKIHLGHYLQIKKMIDLQNAGFDIIILLADLCAYLNQKGELDEIRKIGDYNKKVFEAMGLKAKYVYGSEFQLDKDYTLNVYRLALKTTLKRARRSMELIAREDENPKVAEVIYPIMQVNSAHYRGVDVAVGGMEQRKIHMLARELLPKKVVCIHNPVLTGLDGEGKMSSSKGNFIAVDDSPEEIRAKIKKAYCPAGVVEGNPIMEIAKYFLEYPLTIKRPEKFGGDLTVNSYEELESLFKNKELHPMDLKNAVAEELIKILEPIRKRLLE 308
                                    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

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: Adenine nucleotide alpha hydrolase-like (440)

Superfamily: Nucleotidylyl transferase (325)

Family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain (137)

Protein domain: automated matches (22)

Methanocaldococcus jannaschii [TaxId: 243232] (5)

d4ndaa_

(no "CATH Domain" information available for 4NDA)

(no "Pfam Domain" information available for 4NDA)

Asymmetric Unit(hide GO term definitions)

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 ]
		NIY	[ 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
		Ile A:15 - Ser A:16	[ RasMol ]
		Tyr A:251 - Pro A:252	[ 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
	4nda
		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
	SYY_METJA \| Q57834
		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)
	6.1.1.1
		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
	SYY_METJA \| Q57834
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

4nd6	CRYSTAL STRUCTURE OF APO 3-NITRO-TYROSINE TRNA SYNTHETASE (5B) IN THE OPEN FORM
4nd7	CRYSTAL STRUCTURE OF APO 3-NITRO-TYROSINE TRNA SYNTHETASE (5B) IN THE CLOSED FORM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (4, 4)

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 (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (12, 12)

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