4ISJ - 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 :   RNA LIGASE RTCB IN COMPLEX WITH MN(II)

Authors :   K. K. Desai, C. A. Bingman, G. N. Phillips Jr. , R. T. Raines

Date :   16 Jan 13 (Deposition) - 20 Mar 13 (Release) - 01 May 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.34

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

Keywords :   Rna Ligase, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. K. Desai, C. A. Bingman, G. N. Phillips, R. T. Raines
Structures Of The Noncanonical Rna Ligase Rtcb Reveal The Mechanism Of Histidine Guanylylation.
Biochemistry V. 52 2518 2013
PubMed-ID: 23560983 | Reference-DOI: 10.1021/BI4002375

Molecule 1 - TRNA-SPLICING LIGASE RTCB
	Chains	:	A, B
	EC Number	:	6.5.1.-, 3.1.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQE70
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	MATURE RTCB
	Gene	:	PH1602, RTCB
	Organism Scientific	:	PYROCOCCUS HORIKOSHII
	Organism Taxid	:	70601
	Strain	:	ATCC 700860
	Synonym	:	PHO HYP2 INTEIN

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 17)

No.	Name	Count	Type	Full Name
1	MN	2	Ligand/Ion	MANGANESE (II) ION
2	SO4	13	Ligand/Ion	SULFATE ION
3	SUC	2	Ligand/Ion	SUCROSE

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION
2	SO4	7	Ligand/Ion	SULFATE ION
3	SUC	1	Ligand/Ion	SUCROSE

Biological Unit 2 (2, 7)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION
2	SO4	6	Ligand/Ion	SULFATE ION
3	SUC	1	Ligand/Ion	SUCROSE

Biological Unit 3 (2, 15)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION
2	SO4	13	Ligand/Ion	SULFATE ION
3	SUC	2	Ligand/Ion	SUCROSE

Asymmetric Unit (17, 17)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	CYS A:98 , ASN A:202 , HIS A:234 , HIS A:329 , HOH A:733	BINDING SITE FOR RESIDUE MN A 501
02	AC2	SOFTWARE	ASP A:95 , GLY A:199 , SER A:200 , HIS A:203 , ARG A:238 , HIS A:242 , HOH A:613	BINDING SITE FOR RESIDUE SO4 A 502
03	AC3	SOFTWARE	GLY A:69 , TYR A:70 , GLY A:93 , TYR A:94 , LYS A:351 , HOH A:654 , HOH A:683	BINDING SITE FOR RESIDUE SO4 A 503
04	AC4	SOFTWARE	LYS A:212 , ARG A:472	BINDING SITE FOR RESIDUE SO4 A 504
05	AC5	SOFTWARE	ARG A:366 , ARG A:369	BINDING SITE FOR RESIDUE SO4 A 505
06	AC6	SOFTWARE	GLN A:185 , HOH A:620	BINDING SITE FOR RESIDUE SO4 A 506
07	AC7	SOFTWARE	ARG A:190 , GLN A:194 , GLY A:239 , ALA B:438 , SER B:439 , MET B:440	BINDING SITE FOR RESIDUE SO4 A 507
08	AC8	SOFTWARE	SER A:439 , MET A:440 , ARG A:441 , HOH A:727 , ARG B:412	BINDING SITE FOR RESIDUE SO4 A 508
09	AC9	SOFTWARE	LYS A:17 , ARG A:23 , PRO A:25 , TYR A:57 , LYS A:58 , VAL A:339 , ASP A:340 , HOH A:679 , HOH A:685 , HOH A:697 , HOH A:741	BINDING SITE FOR RESIDUE SUC A 509
10	BC1	SOFTWARE	CYS B:98 , HIS B:234 , HIS B:329 , HOH B:608	BINDING SITE FOR RESIDUE MN B 501
11	BC2	SOFTWARE	ASP B:95 , SER B:200 , HIS B:203 , ARG B:238 , HOH B:604 , HOH B:736	BINDING SITE FOR RESIDUE SO4 B 502
12	BC3	SOFTWARE	TYR B:70 , ILE B:74 , GLY B:93 , TYR B:94 , LYS B:351 , HOH B:644	BINDING SITE FOR RESIDUE SO4 B 503
13	BC4	SOFTWARE	SER B:411 , ARG B:412 , LYS B:413	BINDING SITE FOR RESIDUE SO4 B 504
14	BC5	SOFTWARE	ARG A:257 , ARG B:23 , GLY B:55 , ILE B:56	BINDING SITE FOR RESIDUE SO4 B 505
15	BC6	SOFTWARE	ARG B:366 , ARG B:369	BINDING SITE FOR RESIDUE SO4 B 506
16	BC7	SOFTWARE	ARG A:27 , HOH A:700 , HOH A:759 , LYS B:220	BINDING SITE FOR RESIDUE SO4 B 507
17	BC8	SOFTWARE	LYS B:17 , ARG B:23 , LYS B:58 , ASP B:340 , HOH B:742	BINDING SITE FOR RESIDUE SUC B 508

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

(no "Cis Peptide Bond" information available for 4ISJ)

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

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

(no "Exon" information available for 4ISJ)

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:480
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4isja_ A: Hypothetical protein PH1602                                                                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee....eeee..........eeee.hhhhhhhhhh.hhhhhhhhhh........eeeeeeee......eeeeeeee....eehhhhh......eeeee....hhhhhh.hhhhhhhhhhhhh................hhhhhhhhhhhhhhh...hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh........eeeeeeeeee.hhhhhhhhh.....eeeeeee.hhhhhhhhhhhhhhhhhhhhhhh.....hhhhh.ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeee.eeeeeeeeee..eeeeeeeeee..ee.........hhhhh....eeee.......eeeee.hhhhhhhh..ee........hhhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhh.hhhhhhhhhhhh...eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4isj A   2 VVPLKRIDKIRWEIPKFDKRMRVPGRVYADEVLLEKMKNDRTLEQATNVAMLPGIYKYSIVMPDGHQGYGFPIGGVAAFDVKEGVISPGGIGYDINCGVRLIRTNLTEKEVRPRIKQLVDTLFKNVPSGVGSQGRIKLHWTQIDDVLVDGAKWAVDNGYGWERDLERLEEGGRMEGADPEAVSQRAKQRGAPQLGSLGSGNHFLEVQVVDKIFDPEVAKAYGLFEGQVVVMVHTGSRGLGHQVASDYLRIMERAIRKYRIPWPDRELVSVPFQSEEGQRYFSAMKAAANFAWANRQMITHWVRESFQEVFKQDPEGDLGMDIVYDVAHNIGKVEEHEVDGKRVKVIVHRKGATRAFPPGHEAVPRLYRDVGQPVLIPGSMGTASYILAGTEGAMKETFGSTCHGAGRVLSRKAATRQYRGDRIRQELLNRGIYVRAASMRVVAEEAPGAYKNVDNVVKVVSEAGIAKLVARMRPIGVAKG 481
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481

Chain B from PDB  Type:PROTEIN  Length:480
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4isjb_ B: Hypothetical protein PH1602                                                                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee..eeee..........eeee.hhhhhhhhhhhhhhhhhhhhh........eeeeeeee......eeeeeeee....eehhhhh......eeeeeeeeeehhhhh.hhhhhhhhhhhhh................hhhhhhhhhhhhhhh...hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh........eeeeeeeeee.hhhhhhhhh....eeeeeeee...hhhhhhhhhhhhhhhhhhhhhh..........ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeee.eeeeeeeeee..eeeeeeeeee.eee.........hhhhhh...eeee.......eeeee.hhhhhhhh..eee.......hhhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhh.hhhhhhhhhhhh...eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4isj B   2 VVPLKRIDKIRWEIPKFDKRMRVPGRVYADEVLLEKMKNDRTLEQATNVAMLPGIYKYSIVMPDGHQGYGFPIGGVAAFDVKEGVISPGGIGYDINCGVRLIRTNLTEKEVRPRIKQLVDTLFKNVPSGVGSQGRIKLHWTQIDDVLVDGAKWAVDNGYGWERDLERLEEGGRMEGADPEAVSQRAKQRGAPQLGSLGSGNHFLEVQVVDKIFDPEVAKAYGLFEGQVVVMVHTGSRGLGHQVASDYLRIMERAIRKYRIPWPDRELVSVPFQSEEGQRYFSAMKAAANFAWANRQMITHWVRESFQEVFKQDPEGDLGMDIVYDVAHNIGKVEEHEVDGKRVKVIVHRKGATRAFPPGHEAVPRLYRDVGQPVLIPGSMGTASYILAGTEGAMKETFGSTCHGAGRVLSRKAATRQYRGDRIRQELLNRGIYVRAASMRVVAEEAPGAYKNVDNVVKVVSEAGIAKLVARMRPIGVAKG 481
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481

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: Hypothetical protein PH1602 (7)

Superfamily: Hypothetical protein PH1602 (7)

Family: Hypothetical protein PH1602 (6)

Protein domain: Hypothetical protein PH1602 (5)

Pyrococcus horikoshii [TaxId: 53953] (5)

1a	d4isja_	A:
1b	d4isjb_	B:

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

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

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
		MN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SUC	[ 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 ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]
		BC5	[ RasMol ]	+environment [ RasMol ]
		BC6	[ RasMol ]	+environment [ RasMol ]
		BC7	[ RasMol ]	+environment [ RasMol ]
		BC8	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4isj)

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
	4isj
		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
	RTCB_PYRHO \| O59245
		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)
	3.1.-.-
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc
	6.5.1.-
		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
	RTCB_PYRHO \| O59245
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	RTCB_PYRHO \| O59245	:	1uc2 4dwq 4dwr 4isz 4it0

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 17)

Sites (17, 17)

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, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (16, 16)

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