4DWQ - 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)

Title :   RNA LIGASE RTCB-GMP/MN(2+) COMPLEX

Authors :   C. Okada, S. Xia, M. Englert, M. Yao, D. Soll, J. Wang

Date :   26 Feb 12 (Deposition) - 05 Sep 12 (Release) - 15 Jan 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.25

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

Keywords :   Rtcb, Guanylylation, Rna Ligase, Rtcb-Gmp, Mn2+, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Englert, S. Xia, C. Okada, A. Nakamura, V. Tanavde, M. Yao, S. H. Eom, W. H. Konigsberg, D. Soll, J. Wang
Structural And Mechanistic Insights Into Guanylylation Of Rna-Splicing Ligase Rtcb Joining Rna Between 3'-Terminal Phosphate And 5'-Oh.
Proc. Natl. Acad. Sci. Usa V. 109 15235 2012
PubMed-ID: 22949672 | Reference-DOI: 10.1073/PNAS.1213795109

Molecule 1 - TRNA-SPLICING LIGASE RTCB
	Chains	:	A, B
	EC Number	:	6.5.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	RTCB, PH1602
	Organism Scientific	:	PYROCOCCUS HORIKOSHII
	Organism Taxid	:	53953
	Synonym	:	PHO HYP2 INTEIN

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 15)

No.	Name	Count	Type	Full Name
1	5GP	2	Ligand/Ion	GUANOSINE-5'-MONOPHOSPHATE
2	GOL	2	Ligand/Ion	GLYCEROL
3	MLI	3	Ligand/Ion	MALONATE ION
4	MN	2	Ligand/Ion	MANGANESE (II) ION
5	PO4	5	Ligand/Ion	PHOSPHATE ION
6	POP	1	Ligand/Ion	PYROPHOSPHATE 2-

Biological Unit 1 (5, 8)

No.	Name	Count	Type	Full Name
1	5GP	1	Ligand/Ion	GUANOSINE-5'-MONOPHOSPHATE
2	GOL	1	Ligand/Ion	GLYCEROL
3	MLI	2	Ligand/Ion	MALONATE ION
4	MN	-1	Ligand/Ion	MANGANESE (II) ION
5	PO4	3	Ligand/Ion	PHOSPHATE ION
6	POP	1	Ligand/Ion	PYROPHOSPHATE 2-

Biological Unit 2 (4, 5)

No.	Name	Count	Type	Full Name
1	5GP	1	Ligand/Ion	GUANOSINE-5'-MONOPHOSPHATE
2	GOL	1	Ligand/Ion	GLYCEROL
3	MLI	1	Ligand/Ion	MALONATE ION
4	MN	-1	Ligand/Ion	MANGANESE (II) ION
5	PO4	2	Ligand/Ion	PHOSPHATE ION
6	POP	-1	Ligand/Ion	PYROPHOSPHATE 2-

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN A:202 , PHE A:204 , GLU A:206 , HIS A:234 , HIS A:329 , PRO A:378 , GLY A:379 , SER A:380 , MET A:381 , SER A:385 , HIS A:404 , ALA A:406 , GLY A:407 , GLU A:446 , TYR A:451 , LYS A:480 , MN A:502 , POP A:509 , HOH A:698 , HOH A:764	BINDING SITE FOR RESIDUE 5GP A 501
02	AC2	SOFTWARE	CYS A:98 , HIS A:234 , HIS A:329 , 5GP A:501 , HOH A:807	BINDING SITE FOR RESIDUE MN A 502
03	AC3	SOFTWARE	TYR A:70 , GLY A:93 , TYR A:94 , ASP A:95 , ASN A:330 , LYS A:351	BINDING SITE FOR RESIDUE MLI A 503
04	AC4	SOFTWARE	LYS A:58 , GLU A:338 , MET A:395 , LYS A:396 , GLU A:397 , THR A:398 , PHE A:399 , HOH A:830	BINDING SITE FOR RESIDUE MLI A 504
05	AC5	SOFTWARE	ASN A:106 , GLU A:111 , GLN A:313 , ASP A:318 , LEU A:319 , ARG B:7 , TRP B:13 , GLU B:32 , LYS B:39	BINDING SITE FOR RESIDUE GOL A 505
06	AC6	SOFTWARE	ARG A:190 , GLN A:194 , GLY A:239 , HOH A:706 , HOH A:767 , SER B:439 , MET B:440	BINDING SITE FOR RESIDUE PO4 A 506
07	AC7	SOFTWARE	GLU A:181 , ALA A:182 , SER A:184 , ARG A:280	BINDING SITE FOR RESIDUE PO4 A 507
08	AC8	SOFTWARE	TRP A:162 , GLU A:163 , ARG A:164 , GLU A:316	BINDING SITE FOR RESIDUE PO4 A 508
09	AC9	SOFTWARE	HIS A:67 , ASN A:202 , ARG A:408 , ARG A:412 , TYR A:451 , 5GP A:501	BINDING SITE FOR RESIDUE POP A 509
10	BC1	SOFTWARE	ASN B:202 , PHE B:204 , GLU B:206 , HIS B:234 , HIS B:329 , PRO B:378 , GLY B:379 , SER B:380 , MET B:381 , SER B:385 , HIS B:404 , ALA B:406 , GLY B:407 , TYR B:451 , LYS B:480 , MN B:502 , HOH B:689 , HOH B:761 , HOH B:762	BINDING SITE FOR RESIDUE 5GP B 501
11	BC2	SOFTWARE	CYS B:98 , HIS B:234 , HIS B:329 , 5GP B:501	BINDING SITE FOR RESIDUE MN B 502
12	BC3	SOFTWARE	LYS B:58 , TYR B:59 , GLU B:338 , MET B:395 , LYS B:396 , GLU B:397 , THR B:398 , PHE B:399 , HOH B:769	BINDING SITE FOR RESIDUE MLI B 503
13	BC4	SOFTWARE	LYS A:125 , ARG A:436 , GLN B:134 , GLN B:189 , ARG B:190 , GLN B:194 , PO4 B:506 , HOH B:637	BINDING SITE FOR RESIDUE GOL B 504
14	BC5	SOFTWARE	LYS A:6 , ARG B:104 , ARG B:168 , ALA B:221 , TYR B:222 , TYR B:368	BINDING SITE FOR RESIDUE PO4 B 505
15	BC6	SOFTWARE	ALA A:438 , GLY B:132 , ARG B:190 , GLN B:194 , ARG B:238 , GLY B:239 , GOL B:504	BINDING SITE FOR RESIDUE PO4 B 506

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

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

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	INTEIN_C_TER	PS50818	Intein C-terminal splicing motif profile.	RTCB_PYRHO	465-488	2	A:98-98 B:98-98

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	INTEIN_C_TER	PS50818	Intein C-terminal splicing motif profile.	RTCB_PYRHO	465-488	1	A:98-98 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	INTEIN_C_TER	PS50818	Intein C-terminal splicing motif profile.	RTCB_PYRHO	465-488	1	- B:98-98

(no "Exon" information available for 4DWQ)

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:481
 aligned with RTCB_PYRHO | O59245 from UniProtKB/Swiss-Prot  Length:871

    Alignment length:871
                                    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       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870 
           RTCB_PYRHO     1 MVVPLKRIDKIRWEIPKFDKRMRVPGRVYADEVLLEKMKNDRTLEQATNVAMLPGIYKYSIVMPDGHQGYGFPIGGVAAFDVKEGVISPGGIGYDINCLAPGTRVLTEHGYWLKIEEMPEKFKLQRLRVYNIEEGHNDFSKVVFVAEREVGSEEKAIRIVTESGKVIEGSEDHPVLTPEGYVYLRNVKEGDYILVYPFEGVPYEEKKGVILDESAFEGEDPQVVKFLRERNLIPLQWKDPKVGILARILGFALANGYISENDNLTFHGKEEVLREVRKDLEELGIEAIVAEEDKLKVTSREFAFLLEKLGMAHDSIPEWIIEGPLWIKRNFLAGLFGANGSIVEFKGDVPLPITLTHSRELLNDVSRILEGFKVRAKIKMGKNGSYQLVIEDEDSIRNFLGRINYEYDPEKKARGLIAYAYLKFKELMKGNLMTFEEFARDRGYEGGFVAEKVIEVKSVKPEYDKFYDIGVYHSAHNFIANGIVVHNCGVRLIRTNLTEKEVRPRIKQLVDTLFKNVPSGVGSQGRIKLHWTQIDDVLVDGAKWAVDNGYGWERDLERLEEGGRMEGADPEAVSQRAKQRGAPQLGSLGSGNHFLEVQVVDKIFDPEVAKAYGLFEGQVVVMVHTGSRGLGHQVASDYLRIMERAIRKYRIPWPDRELVSVPFQSEEGQRYFSAMKAAANFAWANRQMITHWVRESFQEVFKQDPEGDLGMDIVYDVAHNIGKVEEHEVDGKRVKVIVHRKGATRAFPPGHEAVPRLYRDVGQPVLIPGSMGTASYILAGTEGAMKETFGSTCHGAGRVLSRKAATRQYRGDRIRQELLNRGIYVRAASMRVVAEEAPGAYKNVDNVVKVVSEAGIAKLVARMRPIGVAKG 871
               SCOP domains d4dwqa_ 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............hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh........eeeeeeeeee.hhhhhhhh......eeeeeee.hhhhhhhhhhhhhhhhhhhhhhh.....hhhhh.ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeee.eeeeeeeeee..eeeeeeeeee.eee.........hhhhh....eeee.......eeeee.hhhhhhhh..eee.......hhhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhh.hhhhhhhhhhhhh..eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------INTEIN_C_TER            ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dwq A   1 MVVPLKRIDKIRWEIPKFDKRMRVPGRVYADEVLLEKMKNDRTLEQATNVAMLPGIYKYSIVMPDGHQGYGFPIGGVAAFDVKEGVISPGGIGYDIN------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGVRLIRTNLTEKEVRPRIKQLVDTLFKNVPSGVGSQGRIKLHWTQIDDVLVDGAKWAVDNGYGWERDLERLEEGGRMEGADPEAVSQRAKQRGAPQLGSLGSGNHFLEVQVVDKIFDPEVAKAYGLFEGQVVVMVHTGSRGLGHQVASDYLRIMERAIRKYRIPWPDRELVSVPFQSEEGQRYFSAMKAAANFAWANRQMITHWVRESFQEVFKQDPEGDLGMDIVYDVAHNIGKVEEHEVDGKRVKVIVHRKGATRAFPPGHEAVPRLYRDVGQPVLIPGSMGTASYILAGTEGAMKETFGSTCHGAGRVLSRKAATRQYRGDRIRQELLNRGIYVRAASMRVVAEEAPGAYKNVDNVVKVVSEAGIAKLVARMRPIGVAKG 481
                                    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       410       420       430       440       450       460       470       480 
                                                                                                                           97                                                                                                                                                                                                                                                                                                                                                                                                     98

Chain B from PDB  Type:PROTEIN  Length:481
 aligned with RTCB_PYRHO | O59245 from UniProtKB/Swiss-Prot  Length:871

    Alignment length:871
                                    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       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870 
           RTCB_PYRHO     1 MVVPLKRIDKIRWEIPKFDKRMRVPGRVYADEVLLEKMKNDRTLEQATNVAMLPGIYKYSIVMPDGHQGYGFPIGGVAAFDVKEGVISPGGIGYDINCLAPGTRVLTEHGYWLKIEEMPEKFKLQRLRVYNIEEGHNDFSKVVFVAEREVGSEEKAIRIVTESGKVIEGSEDHPVLTPEGYVYLRNVKEGDYILVYPFEGVPYEEKKGVILDESAFEGEDPQVVKFLRERNLIPLQWKDPKVGILARILGFALANGYISENDNLTFHGKEEVLREVRKDLEELGIEAIVAEEDKLKVTSREFAFLLEKLGMAHDSIPEWIIEGPLWIKRNFLAGLFGANGSIVEFKGDVPLPITLTHSRELLNDVSRILEGFKVRAKIKMGKNGSYQLVIEDEDSIRNFLGRINYEYDPEKKARGLIAYAYLKFKELMKGNLMTFEEFARDRGYEGGFVAEKVIEVKSVKPEYDKFYDIGVYHSAHNFIANGIVVHNCGVRLIRTNLTEKEVRPRIKQLVDTLFKNVPSGVGSQGRIKLHWTQIDDVLVDGAKWAVDNGYGWERDLERLEEGGRMEGADPEAVSQRAKQRGAPQLGSLGSGNHFLEVQVVDKIFDPEVAKAYGLFEGQVVVMVHTGSRGLGHQVASDYLRIMERAIRKYRIPWPDRELVSVPFQSEEGQRYFSAMKAAANFAWANRQMITHWVRESFQEVFKQDPEGDLGMDIVYDVAHNIGKVEEHEVDGKRVKVIVHRKGATRAFPPGHEAVPRLYRDVGQPVLIPGSMGTASYILAGTEGAMKETFGSTCHGAGRVLSRKAATRQYRGDRIRQELLNRGIYVRAASMRVVAEEAPGAYKNVDNVVKVVSEAGIAKLVARMRPIGVAKG 871
               SCOP domains d4dwqb_ B: Hypothetical protein PH1602                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee....eeee..........eeee.hhhhhhhhhhhhhhhhhhhhh........eeeeeeee......eeeeeeee....eehhhhh.....------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.eeeee....hhhhhh.hhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh........eeeeeeeeee.hhhhhhhh......eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh..........ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeee.eeeeeeeeee..eeeeeeeeee.eee.........hhhhh....eeee.......eeeee.hhhhhhhh..eee.......hhhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhh.hhhhhhhhhhhh...eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------INTEIN_C_TER            ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dwq B   1 MVVPLKRIDKIRWEIPKFDKRMRVPGRVYADEVLLEKMKNDRTLEQATNVAMLPGIYKYSIVMPDGHQGYGFPIGGVAAFDVKEGVISPGGIGYDIN------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGVRLIRTNLTEKEVRPRIKQLVDTLFKNVPSGVGSQGRIKLHWTQIDDVLVDGAKWAVDNGYGWERDLERLEEGGRMEGADPEAVSQRAKQRGAPQLGSLGSGNHFLEVQVVDKIFDPEVAKAYGLFEGQVVVMVHTGSRGLGHQVASDYLRIMERAIRKYRIPWPDRELVSVPFQSEEGQRYFSAMKAAANFAWANRQMITHWVRESFQEVFKQDPEGDLGMDIVYDVAHNIGKVEEHEVDGKRVKVIVHRKGATRAFPPGHEAVPRLYRDVGQPVLIPGSMGTASYILAGTEGAMKETFGSTCHGAGRVLSRKAATRQYRGDRIRQELLNRGIYVRAASMRVVAEEAPGAYKNVDNVVKVVSEAGIAKLVARMRPIGVAKG 481
                                    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       410       420       430       440       450       460       470       480 
                                                                                                                           97                                                                                                                                                                                                                                                                                                                                                                                                     98

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	d4dwqa_	A:
1b	d4dwqb_	B:

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (RTCB_PYRHO | O59245)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0019002	GMP binding	Interacting selectively and non-covalently with GMP, guanosine monophosphate.
	GO:0003972	RNA ligase (ATP) activity	Catalysis of the reaction: ATP + ribonucleotide(n) + ribonucleotide(m) = AMP + diphosphate + ribonucleotide(n+m).
	GO:0008452	RNA ligase activity	Catalysis of the formation of a phosphodiester bond between a hydroxyl group at the end of one RNA chain and the 5'-phosphate group at the end of another.
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	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:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	GO:0030145	manganese ion binding	Interacting selectively and non-covalently with manganese (Mn) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
biological process
	GO:0006396	RNA processing	Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
	GO:0000394	RNA splicing, via endonucleolytic cleavage and ligation	Splicing of RNA via recognition of the folded RNA structure that brings the 5' and 3' splice sites into proximity and cleavage of the RNA at both the 3' and 5' splice sites by an endonucleolytic mechanism, followed by ligation of the exons.
	GO:0016539	intein-mediated protein splicing	The removal of an internal amino acid sequence (an intein) from a protein during protein maturation; the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues.
	GO:0006314	intron homing	Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
	GO:0008033	tRNA processing	The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.

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
		5GP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MLI	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		POP	[ 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 ]

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

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
	4dwq
		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)
	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 4dwr 4isj 4isz 4it0

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 15)

Sites (15, 15)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

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