4JRP - 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 :   STRUCTURE OF E. COLI EXONUCLEASE I IN COMPLEX WITH A 5CY-DT13 OLIGONUCLEOTIDE

Authors :   C. E. Bell

Date :   21 Mar 13 (Deposition) - 08 May 13 (Release) - 03 Jul 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

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

Keywords :   Dna Repair, Dnaq Superfamily, Exonuclease, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. K. Korada, T. D. Johns, C. E. Smith, N. D. Jones, K. A. Mccabe, C. E. Bel
Crystal Structures Of Escherichia Coli Exonuclease I In Complex With Single-Stranded Dna Provide Insights Into The Mechanism Of Processive Digestion.
Nucleic Acids Res. V. 41 5887 2013
PubMed-ID: 23609540 | Reference-DOI: 10.1093/NAR/GKT278

Molecule 1 - 5CY-DT13
	Chains	:	C, D
	Engineered	:	YES
	Other Details	:	CHEMICAL SYNTHESIS
	Synthetic	:	YES

Molecule 2 - EXODEOXYRIBONUCLEASE I
	Chains	:	A, B
	EC Number	:	3.1.11.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET14B
	Expression System Strain	:	BL21(AI)
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	SBCB, CPEA, XONA, B2011, JW1993
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12
	Synonym	:	EXONUCLEASE I, DNA DEOXYRIBOPHOSPHODIESTERASE, DRPASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 20)

No.	Name	Count	Type	Full Name
1	5CY	2	Mod. Nucleotide	1-(3-HYDROXYPROPYL)-2-{(1E,3E,5E)-5-[1-(3-HYDROXYPROPYL)-3,3-DIMETHYL-1,3-DIHYDRO-2H-INDOL-2-YLIDENE]PENTA-1,3-DIEN-1-YL}-3,3-DIMETHYL-3H-INDOLIUM
2	GOL	2	Ligand/Ion	GLYCEROL
3	IPA	1	Ligand/Ion	ISOPROPYL ALCOHOL
4	MG	1	Ligand/Ion	MAGNESIUM ION
5	SO4	14	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 8)

No.	Name	Count	Type	Full Name
1	5CY	1	Mod. Nucleotide	1-(3-HYDROXYPROPYL)-2-{(1E,3E,5E)-5-[1-(3-HYDROXYPROPYL)-3,3-DIMETHYL-1,3-DIHYDRO-2H-INDOL-2-YLIDENE]PENTA-1,3-DIEN-1-YL}-3,3-DIMETHYL-3H-INDOLIUM
2	GOL	2	Ligand/Ion	GLYCEROL
3	IPA	-1	Ligand/Ion	ISOPROPYL ALCOHOL
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 11)

No.	Name	Count	Type	Full Name
1	5CY	1	Mod. Nucleotide	1-(3-HYDROXYPROPYL)-2-{(1E,3E,5E)-5-[1-(3-HYDROXYPROPYL)-3,3-DIMETHYL-1,3-DIHYDRO-2H-INDOL-2-YLIDENE]PENTA-1,3-DIEN-1-YL}-3,3-DIMETHYL-3H-INDOLIUM
2	GOL	-1	Ligand/Ion	GLYCEROL
3	IPA	1	Ligand/Ion	ISOPROPYL ALCOHOL
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	SO4	9	Ligand/Ion	SULFATE ION

Biological Unit 3 (4, 19)

No.	Name	Count	Type	Full Name
1	5CY	2	Mod. Nucleotide	1-(3-HYDROXYPROPYL)-2-{(1E,3E,5E)-5-[1-(3-HYDROXYPROPYL)-3,3-DIMETHYL-1,3-DIHYDRO-2H-INDOL-2-YLIDENE]PENTA-1,3-DIEN-1-YL}-3,3-DIMETHYL-3H-INDOLIUM
2	GOL	2	Ligand/Ion	GLYCEROL
3	IPA	1	Ligand/Ion	ISOPROPYL ALCOHOL
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	SO4	14	Ligand/Ion	SULFATE ION

Asymmetric Unit (18, 18)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:15 , HOH A:610 , HOH A:611 , HOH A:735 , DT C:12 , DT C:13	BINDING SITE FOR RESIDUE MG C 101
02	AC2	SOFTWARE	LYS A:214 , HIS A:215 , MET A:218 , ARG A:256 , HOH A:601 , HIS B:215 , ARG B:256 , HOH B:672 , HOH B:695	BINDING SITE FOR RESIDUE SO4 A 501
03	AC3	SOFTWARE	ARG A:106 , SER A:233 , MET A:235 , LYS A:299 , LEU A:300 , HIS A:302 , HOH A:644 , HOH A:720 , HOH A:746 , HOH A:749	BINDING SITE FOR RESIDUE SO4 A 502
04	AC4	SOFTWARE	PHE A:415 , PRO A:416 , GLY A:417	BINDING SITE FOR RESIDUE SO4 A 503
05	AC5	SOFTWARE	ARG A:148 , ARG A:203 , ARG A:316 , HOH A:682	BINDING SITE FOR RESIDUE SO4 A 504
06	AC6	SOFTWARE	ARG A:35 , GLY A:44 , GLU A:45 , GLU A:47 , LEU A:91 , HOH A:740 , HOH A:741	BINDING SITE FOR RESIDUE SO4 A 505
07	AC7	SOFTWARE	THR A:436 , PRO A:437 , GLU A:438 , HIS B:430 , GLN B:433	BINDING SITE FOR RESIDUE GOL A 506
08	AC8	SOFTWARE	HIS A:430 , GLN A:433 , HOH A:675 , THR B:436 , GLU B:438	BINDING SITE FOR RESIDUE GOL A 507
09	AC9	SOFTWARE	ARG B:148 , ARG B:203 , ALA B:393	BINDING SITE FOR RESIDUE SO4 B 501
10	BC1	SOFTWARE	THR B:210 , HIS B:211 , LYS B:216 , ARG B:389 , ASN B:390	BINDING SITE FOR RESIDUE SO4 B 502
11	BC2	SOFTWARE	HIS B:22 , PRO B:23 , ALA B:24 , LEU B:25 , HOH B:751	BINDING SITE FOR RESIDUE SO4 B 503
12	BC3	SOFTWARE	ASN B:414 , PHE B:415 , PRO B:416 , GLY B:417 , HOH B:719	BINDING SITE FOR RESIDUE SO4 B 504
13	BC4	SOFTWARE	ASN B:157 , SER B:163 , PHE B:164 , ARG B:165 , HIS B:168	BINDING SITE FOR RESIDUE SO4 B 505
14	BC5	SOFTWARE	PRO B:228 , LEU B:334 , ARG B:338	BINDING SITE FOR RESIDUE SO4 B 506
15	BC6	SOFTWARE	LYS A:216 , SER B:373 , ASP B:374 , HOH B:688	BINDING SITE FOR RESIDUE SO4 B 507
16	BC7	SOFTWARE	ARG B:200	BINDING SITE FOR RESIDUE SO4 B 508
17	BC8	SOFTWARE	GLN B:129 , LYS B:381 , HOH B:601 , HOH B:602 , 5CY D:0	BINDING SITE FOR RESIDUE SO4 B 509
18	BC9	SOFTWARE	PHE A:439 , GLY A:442 , TYR A:443 , HOH A:690 , GLY B:442 , TYR B:443	BINDING SITE FOR RESIDUE IPA B 510

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

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

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

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

(no "Exon" information available for 4JRP)

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:460
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee.........eeeeeeeeee.........eeee.........hhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhh...eeee......hhhhhhhhhhhhh....hhhhhhhhhee.hhhhhhhhhhhhh................hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh.........eeee.hhhhhhhh.eeeeeeeee......eeeeee....hhhhhhhhhhhhhhhhh.............eeeee.....eeee.hhhhhhhhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhh.....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jrp A   7 QQSTFLFHDYETFGTHPALDRPAQFAAIRTDSEFNVIGEPEVFYCKPADDYLPQPGAVLITGITPQEARAKGENEAAFAARIHSLFTVPKTCILGYNNVRFDDEVTRNIFYRNFYDPYAWSWQHDNSRWDLLDVMRACYALRPEGINWPENDDGLPSFRLEHLTKANGIEHDAMADVYATIAMAKLVKTRQPRLFDYLFTHRNKHKLMALIDVPQMKPLVHVSGMFGAWRGNTSWVAPLAWHPENRNAVIMVDLAGDISPLLELDSDTLRERLYTAKTDLGDNAAVPVKLVHINKCPVLAQANTLRPEDADRLGINRQHCLDNLKILRENPQVREKVVAIFAEASDNVDAQLYNGFFSDADRAAMKIVLETEPRNLPALDITFVDKRIEKLLFNYRARNFPGTLDYAEQQRWLEHRRQVFTPEFLQGYADELQMLVQQYADDKEKVALLKALWQYAEEIV 475
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176|      190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350   ||  365       375       385       395       405       415       425       435       445       455       465       475
                                                                                                                                                                                                   176|                                                                                                                                                                          354|                                                                                                                   
                                                                                                                                                                                                    181                                                                                                                                                                           360

Chain B from PDB  Type:PROTEIN  Length:465
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee.........eeeeeeeeee....eeeeeeeee.........hhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhhh....hhhhhhhhhee.hhhhhhhhhhhhh................hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh.........eeee.hhhhhhhh.eeeeeeeee......eeeeee....hhhhhhhhhhhhhhhhh.............eeeee.hhh.eeee.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jrp B   7 QQSTFLFHDYETFGTHPALDRPAQFAAIRTDSEFNVIGEPEVFYCKPADDYLPQPGAVLITGITPQEARAKGENEAAFAARIHSLFTVPKTCILGYNNVRFDDEVTRNIFYRNFYDPYAWSWQHDNSRWDLLDVMRACYALRPEGINWPENDDGLPSFRLEHLTKANGIEHDAMADVYATIAMAKLVKTRQPRLFDYLFTHRNKHKLMALIDVPQMKPLVHVSGMFGAWRGNTSWVAPLAWHPENRNAVIMVDLAGDISPLLELDSDTLRERLYTAKTDLGDNAAVPVKLVHINKCPVLAQANTLRPEDADRLGINRQHCLDNLKILRENPQVREKVVAIFAEAEPFTPSDNVDAQLYNGFFSDADRAAMKIVLETEPRNLPALDITFVDKRIEKLLFNYRARNFPGTLDYAEQQRWLEHRRQVFTPEFLQGYADELQMLVQQYADDKEKVALLKALWQYAEEIV 475
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176||     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     
                                                                                                                                                                                                    177|                                                                                                                                                                                                                                                                                                     
                                                                                                                                                                                                     182

Chain C from PDB  Type:DNA  Length:14
                                              
                 4jrp C   0 xTTTTTTTTTTTTT  13
                            |        9    
                            0-5CY

Chain D from PDB  Type:DNA  Length:14
                                              
                 4jrp D   0 xTTTTTTTTTTTTT  13
                            |        9    
                            0-5CY

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 '\|'

(no "SCOP Domain" information available for 4JRP)

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

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

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
		5CY	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		IPA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ 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 ]
		BC9	[ RasMol ]	+environment [ RasMol ]

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

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
	4jrp
		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
	EX1_ECOLI \| P04995
		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)
	3.1.11.1
		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
	EX1_ECOLI \| P04995
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	EX1_ECOLI \| P04995	:	1fxx 2qxf 3c94 3c95 3hl8 3hp9 4hcb 4hcc 4jrq 4js4 4js5

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 20)

Sites (18, 18)

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 (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (19, 19)

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