1TD5 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE LIGAND BINDING DOMAIN OF E. COLI ICLR.

Authors :   J. R. Walker, L. Evdokimova, R. -G. Zhang, A. Bochkarev, A. Joachimiak, C. Arrowsmith, A. Edwards, A. Savchenko, Midwest Center For Structural Genomics (Mcsg)

Date :   21 May 04 (Deposition) - 13 Jul 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Midwest Center For Structural Genomics, Alpha/Beta Domain, Ligand Binding Domain, Transcription Regulator, Psi, Protein Structure Initiative, Mcsg (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. R. Walker, L. Evdokimova, R. -G. Zhang, A. Bochkarev, C. Arrowsmith, A. Edwards, A. Savchenko
Structural Analyses Of The Ligand Binding Sites Of The Iclr Family Of Transcriptional Regulators
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - ACETATE OPERON REPRESSOR
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Fragment	:	LIGAND BINDING DOMAIN
	Gene	:	ICLR, B4018
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	APC5050

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 32)

No.	Name	Count	Type	Full Name
1	MSE	32	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 8)

No.	Name	Count	Type	Full Name
1	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 8)

No.	Name	Count	Type	Full Name
1	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 3 (1, 8)

No.	Name	Count	Type	Full Name
1	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 4 (1, 8)

No.	Name	Count	Type	Full Name
1	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 1TD5)

(no "SS Bond" information available for 1TD5)

(no "Cis Peptide Bond" information available for 1TD5)

(no "SAP(SNP)/Variant" information available for 1TD5)

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ICLR_ED	PS51078	IclR effector binding domain profile.	ICLR_ECOLI	87-272	3	A:4-178 B:4-178 D:4-178

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ICLR_ED	PS51078	IclR effector binding domain profile.	ICLR_ECOLI	87-272	1	A:4-178 - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ICLR_ED	PS51078	IclR effector binding domain profile.	ICLR_ECOLI	87-272	1	- B:4-178 -

Biological Unit 3 (, 0)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ICLR_ED	PS51078	IclR effector binding domain profile.	ICLR_ECOLI	87-272	0	- - -

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ICLR_ED	PS51078	IclR effector binding domain profile.	ICLR_ECOLI	87-272	1	- - D:4-178

(no "Exon" information available for 1TD5)

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:179
 aligned with ICLR_ECOLI | P16528 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:194
                                    89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269    
           ICLR_ECOLI    80 GHWAIGAHAFMVGSSFLQSRNLLAIVHPILRNLMEESGETVNMAVLDQSDHEAIIIDQVQCTHLMRMSAPIGGKLPMHASGAGKAFLAQLSEEQVTKLLHRKGLHAYTHATLVSPVHLKEDLAQTRKRGYSFDDEEHALGLRCLAACIFDEHREPFAAISISGPISRITDDRVTEFGAMVIKAAKEVTLAYGGM 273
               SCOP domains d1               td5a_ A: Transcriptional regulator IclR, C-terminal domain                                                                                                                        SCOP domains
               CATH domains 1t               d5A00 A:1-178  [code=3.30.450.40, no name defined]                                                                                                                              - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..---------------.hhhhhhhhhhhhhhhhhhhh.eeeeeeee....eeeeeeee.....eee......ee....hhhhhhhhh..hhhhhhhhhhhh...........hhhhhhhhhhhhhhhh...ee......eeeeeeeee.....eeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------ICLR_ED  PDB: A:4-178 UniProt: 87-272                                                                                                                                                     - PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1td5 A   1 GH---------------mSRNLLAIVHPILRNLmEESGETVNmAVLDQSDHEAIIIDQVQCTHLmRmSAPIGGKLPmHASGAGKAFLAQLSEEQVTKLLHRKGLHAYTHATLVSPVHLKEDLAQTRKRGYSFDDEEHALGLRCLAACIFDEHREPFAAISISGPISRITDDRVTEFGAmVIKAAKEVTLAYGGm 179
                             |       -       | 5        15   |    25  |     35        45    | | 55      | 65        75        85        95       105       115       125       135       145       155       165       175   |
                             2               3-MSE          19-MSE   28-MSE                50-MSE      62-MSE                                                                                               164-MSE        179-MSE
                                                                                             52-MSE

Chain B from PDB  Type:PROTEIN  Length:179
 aligned with ICLR_ECOLI | P16528 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:194
                                    89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269    
           ICLR_ECOLI    80 GHWAIGAHAFMVGSSFLQSRNLLAIVHPILRNLMEESGETVNMAVLDQSDHEAIIIDQVQCTHLMRMSAPIGGKLPMHASGAGKAFLAQLSEEQVTKLLHRKGLHAYTHATLVSPVHLKEDLAQTRKRGYSFDDEEHALGLRCLAACIFDEHREPFAAISISGPISRITDDRVTEFGAMVIKAAKEVTLAYGGM 273
               SCOP domains d1               td5b_ B: Transcriptional regulator IclR, C-terminal domain                                                                                                                        SCOP domains
               CATH domains 1t               d5B00 B:1-178  [code=3.30.450.40, no name defined]                                                                                                                              - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..---------------.hhhhhhhhhhhhhhhhhhhh.eeeeeeee....eeeeeeee.....eee......ee....hhhhhhhhhh.hhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh.eeee......eeeeeeeee.....eeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------ICLR_ED  PDB: B:4-178 UniProt: 87-272                                                                                                                                                     - PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1td5 B   1 GH---------------mSRNLLAIVHPILRNLmEESGETVNmAVLDQSDHEAIIIDQVQCTHLmRmSAPIGGKLPmHASGAGKAFLAQLSEEQVTKLLHRKGLHAYTHATLVSPVHLKEDLAQTRKRGYSFDDEEHALGLRCLAACIFDEHREPFAAISISGPISRITDDRVTEFGAmVIKAAKEVTLAYGGm 179
                             |       -       | 5        15   |    25  |     35        45    | | 55      | 65        75        85        95       105       115       125       135       145       155       165       175   |
                             2               3-MSE          19-MSE   28-MSE                50-MSE      62-MSE                                                                                               164-MSE        179-MSE
                                                                                             52-MSE

Chain C from PDB  Type:PROTEIN  Length:178
 aligned with ICLR_ECOLI | P16528 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:178
                                   105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265        
           ICLR_ECOLI    96 LQSRNLLAIVHPILRNLMEESGETVNMAVLDQSDHEAIIIDQVQCTHLMRMSAPIGGKLPMHASGAGKAFLAQLSEEQVTKLLHRKGLHAYTHATLVSPVHLKEDLAQTRKRGYSFDDEEHALGLRCLAACIFDEHREPFAAISISGPISRITDDRVTEFGAMVIKAAKEVTLAYGGM 273
               SCOP domains d1td5c_ C: Transcriptional regulator IclR, C-terminal domain                                                                                                                       SCOP domains
               CATH domains 1td5C00 C:2-178  [code=3.30.450.40, no name defined]                                                                                                                             - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh.eeeeeeee....eeeeeeee.....eee......ee....hhhhhhhhh..hhhhhhhhhhh............hhhhhhhhhhhhhhhh.eeee......eeeeeeeee.....eeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ICLR_ED  PDB: - UniProt: 87-272                                                                                                                                                  - PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1td5 C   2 HmSRNLLAIVHPILRNLmEESGETVNmAVLDQSDHEAIIIDQVQCTHLmRmSAPIGGKLPmHASGAGKAFLAQLSEEQVTKLLHRKGLHAYTHATLVSPVHLKEDLAQTRKRGYSFDDEEHALGLRCLAACIFDEHREPFAAISISGPISRITDDRVTEFGAmVIKAAKEVTLAYGGm 179
                             |      11       |21      | 31        41        51|       61|       71        81        91       101       111       121       131       141       151       161  |    171       |
                             |              19-MSE   28-MSE                50-MSE      62-MSE                                                                                               164-MSE        179-MSE
                             3-MSE                                           52-MSE

Chain D from PDB  Type:PROTEIN  Length:180
 aligned with ICLR_ECOLI | P16528 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:195
                                    89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269     
           ICLR_ECOLI    80 GHWAIGAHAFMVGSSFLQSRNLLAIVHPILRNLMEESGETVNMAVLDQSDHEAIIIDQVQCTHLMRMSAPIGGKLPMHASGAGKAFLAQLSEEQVTKLLHRKGLHAYTHATLVSPVHLKEDLAQTRKRGYSFDDEEHALGLRCLAACIFDEHREPFAAISISGPISRITDDRVTEFGAMVIKAAKEVTLAYGGMR 274
               SCOP domains d1               td5d_ D: Transcriptional regulator IclR, C-terminal domain                                                                                                                         SCOP domains
               CATH domains 1t               d5D00 D:1-180  [code=3.30.450.40, no name defined]                                                                                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..---------------.hhhhhhhhhhhhhhhhhhhh.eeeeeee......eeeeeee.....eee......ee....hhhhhhhhh..hhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh.eeee......eeeeeeeee.....eeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------ICLR_ED  PDB: D:4-178 UniProt: 87-272                                                                                                                                                     -- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1td5 D   1 GH---------------mSRNLLAIVHPILRNLmEESGETVNmAVLDQSDHEAIIIDQVQCTHLmRmSAPIGGKLPmHASGAGKAFLAQLSEEQVTKLLHRKGLHAYTHATLVSPVHLKEDLAQTRKRGYSFDDEEHALGLRCLAACIFDEHREPFAAISISGPISRITDDRVTEFGAmVIKAAKEVTLAYGGmR 180
                             |       -       | 5        15   |    25  |     35        45    | | 55      | 65        75        85        95       105       115       125       135       145       155       165       175   | 
                             2               3-MSE          19-MSE   28-MSE                50-MSE      62-MSE                                                                                               164-MSE        179-MSE
                                                                                             52-MSE

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: Profilin-like (304)

Superfamily: GAF domain-like (54)

Family: IclR ligand-binding domain-like (5)

Protein domain: Transcriptional regulator IclR, C-terminal domain (4)

Escherichia coli [TaxId: 562] (3)

1a	d1td5a_	A:
1b	d1td5c_	C:
1c	d1td5d_	D:
1d	d1td5b_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Beta-Lactamase (202)

Homologous Superfamily: [code=3.30.450.40, no name defined] (27)

Escherichia coli. Organism_taxid: 562. (5)

1a	1td5C00	C:2-178
1b	1td5A00	A:1-178
1c	1td5B00	B:1-178
1d	1td5D00	D:1-180

(no "Pfam Domain" information available for 1TD5)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (ICLR_ECOLI | P16528)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
	GO:0006097	glyoxylate cycle	A modification of the TCA cycle occurring in some plants and microorganisms, in which isocitrate is cleaved to glyoxylate and succinate. Glyoxylate can then react with acetyl-CoA to form malate.
	GO:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
(no "Sites" information available for 1td5)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1td5)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]
		Biological Unit 4	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 2 PNG format \| Biol. Unit 3 PNG format \| Biol. Unit 4 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
	1td5
		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
	ICLR_ECOLI \| P16528
		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
	ICLR_ECOLI \| P16528
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	ICLR_ECOLI \| P16528	:	2o99 2o9a

1t9l	CRYSTAL STRUCTURE OF THE E. COLI GLYOXYLATE REGULATORY PROTEIN LIGAND BINDING DOMAIN COMPLEXED WITH GLYOXYLATE.
1tf1	CRYSTAL STRUCTURE OF THE E. COLI GLYOXYLATE REGULATORY PROTEIN LIGAND BINDING DOMAIN RELATED ID: APC5050 RELATED DB: TARGETDB

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 32)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 3)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (1, 4)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

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