4OAT - 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 :   THE CRYSTAL STRUCTURE OF A SOLUTE-BINDING PROTEIN (N280D MUTANT) FROM ANABAENA VARIABILIS ATCC 29413 IN COMPLEX WITH ISOLEUCINE.

Authors :   K. Tan, H. Li, R. Jedrzejczak, A. Joachimiak, Midwest Center For Str Genomics (Mcsg)

Date :   06 Jan 14 (Deposition) - 15 Jan 14 (Release) - 15 Jan 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.20

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

Keywords :   Structural Genomics, Psi-Biology, Midwest Center For Structuralgenomics, Mcsg, Protein Structure Initiative, Transport Protein, Midwest Center For Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Tan, H. Li, R. Jedrzejczak, A. Joachimiak
The Crystal Structure Of A Solute-Binding Protein (N280D Mutant) From Anabaena Variabilis Atcc 29413 In Complex With Isoleucine.
To Be Published
PubMed: search

Molecule 1 - AMINO ACID/AMIDE ABC TRANSPORTER SUBSTRATE-BINDING PROTEIN, HAAT FAMILY
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMCSG68
	Expression System Strain	:	BL21-GOLD(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	AVA_0465
	Mutation	:	YES
	Organism Scientific	:	ANABAENA VARIABILIS
	Organism Taxid	:	240292
	Strain	:	ATCC 29413

		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 (4, 8)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	ILE	2	Mod. Amino Acid	ISOLEUCINE
3	MG	2	Ligand/Ion	MAGNESIUM ION
4	MSE	2	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	ILE	1	Mod. Amino Acid	ISOLEUCINE
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	MSE	1	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	ILE	1	Mod. Amino Acid	ISOLEUCINE
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	MSE	1	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:130 , LEU A:131 , SER A:132 , SER A:153 , ASN A:154 , THR A:155 , PHE A:204 , ASP A:280 , GLY A:281 , HOH A:671	BINDING SITE FOR RESIDUE ILE A 501
2	AC2	SOFTWARE	ASP A:233 , THR A:234 , ASP A:235 , HOH A:837 , THR B:234 , HOH B:690	BINDING SITE FOR RESIDUE CL A 502
3	AC3	SOFTWARE	PRO A:160 , GLY A:163 , VAL A:166 , ILE A:388 , HOH A:641	BINDING SITE FOR RESIDUE MG A 503
4	AC4	SOFTWARE	THR B:130 , LEU B:131 , SER B:132 , SER B:153 , ASN B:154 , THR B:155 , PHE B:204 , ASP B:280 , GLY B:281 , HOH B:613	BINDING SITE FOR RESIDUE ILE B 501
5	AC5	SOFTWARE	ASP B:233 , THR B:234 , ASP B:235 , HOH B:859 , HOH B:916	BINDING SITE FOR RESIDUE CL B 502
6	AC6	SOFTWARE	PRO B:160 , GLY B:163 , VAL B:166 , ILE B:388 , HOH B:717	BINDING SITE FOR RESIDUE MG B 503

Asymmetric Unit

No.	Residues
1	A:291	-	A:295
2	B:291	-	B:295

Asymmetric Unit

No.	Residues
1	Gly A:128	-	Pro A:129
2	Gly B:128	-	Pro B:129

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

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

(no "Exon" information available for 4OAT)

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:365
                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4oata_ A: automated matches                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.......hhhhhhhhhhhhhhhhhhhhhh.......eeeee.....hhhhhhhhhhhhhhh.....ee...hhhhhhhhhhhhhhhh..eee.......hhhhh..eee...hhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhhhhh..eeeeeeee......hhhhhhhhhh....eeeee.hhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeee..eeeee.....ee....eeeeeee......eeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oat A  53 NTIPIGIALAQTSNVALLGQEQVAGAKIAEKYFNDKGGVNGTPIKLIFQDTAGDEAGTINAFQTLINKDKVVGIVGPTLSQQAFSANPIAERAKVPVVGPSNTAKGIPEIGDYVARVSAPVSVVAPNSVKAALKQNPNIKKVAVFFAQNDAFSKSETEIFQQTVKDQGLELVTVQKFQTTDTDFQSQATNAINLKPDLVIISGLAADGGNLVRQLRELGYQGAIIGGDGLNTSNVFAVCKALCDGVLIAQAYSPEYTGEINKAFRQAYVDQYKKEPPQFSAQAFAAVQVYVESLKALDTKNKVSKIQLPELRTELNKQLLTGKYNTPLGEISFTPIGEVVQKDFYVAQIKmEKDGSQGKFTFLKI 501
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402|      412   ||
                                                                                                                                                                                                                                                                                                                                                                                        403-MSE      416|
                                                                                                                                                                                                                                                                                                                                                                                                      501

Chain B from PDB  Type:PROTEIN  Length:365
                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4oatb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.......hhhhhhhhhhhhhhhhhhhhhh.......eeeee.....hhhhhhhhhhhhhhh.....ee...hhhhhhhhhhhhhhhh..eee.......hhhhh..eee...hhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhhhhhh.eeeeeeee......hhhhhhhhhh....eeeee.hhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeee..eeeee.....ee....eeeeeee......eeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oat B  53 NTIPIGIALAQTSNVALLGQEQVAGAKIAEKYFNDKGGVNGTPIKLIFQDTAGDEAGTINAFQTLINKDKVVGIVGPTLSQQAFSANPIAERAKVPVVGPSNTAKGIPEIGDYVARVSAPVSVVAPNSVKAALKQNPNIKKVAVFFAQNDAFSKSETEIFQQTVKDQGLELVTVQKFQTTDTDFQSQATNAINLKPDLVIISGLAADGGNLVRQLRELGYQGAIIGGDGLNTSNVFAVCKALCDGVLIAQAYSPEYTGEINKAFRQAYVDQYKKEPPQFSAQAFAAVQVYVESLKALDTKNKVSKIQLPELRTELNKQLLTGKYNTPLGEISFTPIGEVVQKDFYVAQIKmEKDGSQGKFTFLKI 501
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402|      412   ||
                                                                                                                                                                                                                                                                                                                                                                                        403-MSE      416|
                                                                                                                                                                                                                                                                                                                                                                                                      501

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Periplasmic binding protein-like I (179)

Superfamily: Periplasmic binding protein-like I (179)

Family: automated matches (65)

Protein domain: automated matches (65)

Anabaena variabilis [TaxId: 240292] (6)

1a	d4oata_	A:
1b	d4oatb_	B:

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

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

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
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ILE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MSE	[ 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 ]

	Cis Peptide Bonds
		Gly A:128 - Pro A:129	[ RasMol ]
		Gly B:128 - Pro B:129	[ RasMol ]

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
	4oat
		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
	Q3MFZ5_ANAVT \| Q3MFZ5
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

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
	Q3MFZ5_ANAVT \| Q3MFZ5
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/TrEMBL
	Q3MFZ5_ANAVT \| Q3MFZ5	:	4nqr 4nv3 4obb 4og2 4otz 4qym 4rdc 4rv5

4nqr	N280D MUTANT IN COMPLEX WITH ALANINE
4nv3	N280D MUTANT IN COMPLEX WITH VALINE RELATED ID: MCSG-APC110063 RELATED DB: TARGETTRACK

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 8)

Sites (6, 6)

SS Bonds (2, 2)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (2, 2)

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