Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  THE CRYSTAL STRUCTURE OF A SOLUTE-BINDING PROTEIN FROM ANABAENA VARIABILIS ATCC 29413 IN COMPLEX WITH PYRUVIC ACID
 
Authors :  K. Tan, H. Li, R. Jedrzejczak, A. Joachimiak, Midwest Center For Str Genomics (Mcsg)
Date :  24 Nov 14  (Deposition) - 10 Dec 14  (Release) - 28 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.04
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Structural Genomics, Psi-Biology, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Tan, H. Li, R. Jedrzejczak, A. Joachimiak
The Crystal Structure Of A Solute-Binding Protein From Anabaena Variabilis Atcc 29413 In Complex With Pyruvic Acid
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - AMINO ACID/AMIDE ABC TRANSPORTER SUBSTRATE-BINDING PROTEIN, HAAT FAMILY
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG73
    Expression System Strain: BL21-GOLD(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: AVA_0465
    Organism Scientific: ANABAENA VARIABILIS ATCC 29413
    Organism Taxid: 240292
    Strain: ATCC 29413

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric Unit (4, 7)
No.NameCountTypeFull Name
1FMT1Ligand/IonFORMIC ACID
2MG2Ligand/IonMAGNESIUM ION
3MSE2Mod. Amino AcidSELENOMETHIONINE
4PYR2Ligand/IonPYRUVIC ACID
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1FMT1Ligand/IonFORMIC ACID
2MG-1Ligand/IonMAGNESIUM ION
3MSE1Mod. Amino AcidSELENOMETHIONINE
4PYR1Ligand/IonPYRUVIC ACID
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1FMT-1Ligand/IonFORMIC ACID
2MG-1Ligand/IonMAGNESIUM ION
3MSE1Mod. Amino AcidSELENOMETHIONINE
4PYR1Ligand/IonPYRUVIC ACID

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:131 , SER A:132 , SER A:153 , ASN A:154 , THR A:155 , PHE A:204 , ASN A:280 , HOH A:613BINDING SITE FOR RESIDUE PYR A 501
2AC2SOFTWAREPRO A:160 , GLY A:163 , VAL A:166 , ILE A:388 , HOH A:660BINDING SITE FOR RESIDUE MG A 502
3AC3SOFTWAREASN A:283 , GLN A:302 , PRO A:329 , GLN A:330 , PHE A:412 , HOH A:689 , HOH A:690 , HOH A:744 , HOH A:763BINDING SITE FOR RESIDUE FMT A 503
4AC4SOFTWARELEU B:131 , SER B:132 , SER B:153 , ASN B:154 , THR B:155 , PHE B:204 , ASN B:280 , HOH B:624BINDING SITE FOR RESIDUE PYR B 501
5AC5SOFTWAREPRO B:160 , GLY B:163 , VAL B:166 , ILE B:388 , HOH B:629BINDING SITE FOR RESIDUE MG B 502

(-) SS Bonds  (2, 2)

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

(-) Cis Peptide Bonds  (2, 2)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4RV5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4RV5)

(-) Exons   (0, 0)

(no "Exon" information available for 4RV5)

(-) Sequences/Alignments

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:364
                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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
                 4rv5 A  53 NTIPIGIALAQTSNVALLGQEQVAGAKIAEKYFNDKGGVNGTPIKLIFQDTAGDEAGTINAFQTLINKDKVVGIVGPTLSQQAFSANPIAERAKVPVVGPSNTAKGIPEIGDYVARVSAPVSVVAPNSVKAALKQNPNIKKVAVFFAQNDAFSKSETEIFQQTVKDQGLELVTVQKFQTTDTDFQSQATNAINLKPDLVIISGLAADGGNLVRQLRELGYQGAIIGGNGLNTSNVFAVCKALCDGVLIAQAYSPEYTGEINKAFRQAYVDQYKKEPPQFSAQAFAAVQVYVESLKALDTKNKVSKIQLPELRTELNKQLLTGKYNTPLGEISFTPIGEVVQKDFYVAQIKmEKDGSQGKFTFLK 416
                                    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         


Chain B from PDB  Type:PROTEIN  Length:364
                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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
                 4rv5 B  53 NTIPIGIALAQTSNVALLGQEQVAGAKIAEKYFNDKGGVNGTPIKLIFQDTAGDEAGTINAFQTLINKDKVVGIVGPTLSQQAFSANPIAERAKVPVVGPSNTAKGIPEIGDYVARVSAPVSVVAPNSVKAALKQNPNIKKVAVFFAQNDAFSKSETEIFQQTVKDQGLELVTVQKFQTTDTDFQSQATNAINLKPDLVIISGLAADGGNLVRQLRELGYQGAIIGGNGLNTSNVFAVCKALCDGVLIAQAYSPEYTGEINKAFRQAYVDQYKKEPPQFSAQAFAAVQVYVESLKALDTKNKVSKIQLPELRTELNKQLLTGKYNTPLGEISFTPIGEVVQKDFYVAQIKmEKDGSQGKFTFLK 416
                                    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
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4RV5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4RV5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4RV5)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

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
    FMT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PYR  [ 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 ]
 
  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 ]

(-) Still Images

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)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4rv5
    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

(-) Analysis Tools

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)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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

(-) Related Entries Specified in the PDB File

4nqr N280D MUTANT IN COMPLEX WITH ALANINE
4nv3 N280D MUTANT IN COMPLEX WITH VALINE
4oat N280D MUTANT IN COMPLEX WITH ISOLEUCINE
4obb IN COMPLEX WITH (3S)-3-METHYL-2-OXOPENTANOIC ACID
4og2 N280D MUTANT IN COMPLEX WITH LEUCINE
4otz N280D MUTANT IN COMPLEX WITH CYSTEIN
4qym N280D MUTANT IN COMPLEX WITH METHIONINE
4rdc N280D MUTANT IN COMPLEX WITH PROLINE RELATED ID: MCSG-APC110063 RELATED DB: TARGETTRACK