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
(-)Biological Unit 3
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)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF LYSR SUBSTRATE BINDING DOMAIN (25-263) OF PUTATIVE PERIPLASMIC PROTEIN FROM WOLINELLA SUCCINOGENES
 
Authors :  Y. Kim, L. Volkart, J. Bearden, A. Joachimiak, Midwest Center For St Genomics (Mcsg)
Date :  11 Nov 09  (Deposition) - 01 Dec 09  (Release) - 21 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.41
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Alpha-Beta Structure, Periplasmic Binding Protein Fold, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kim, L. Volkart, J. Bearden, A. Joachimiak
Crystal Structure Of Lysr Substrate Binding Domain From Wolinella Succinogenes
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE PERIPLASMIC PROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PMCSG19
    Expression System Strain: BL21 MAGIC
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: LYSR SUBSTRATE BINDING DOMAIN
    Gene: WS1370
    Organism Scientific: WOLINELLA SUCCINOGENES
    Organism Taxid: 844
    Strain: DSMZ 1740
    Synonym: LYSR SUBSTRATE BINDING DOMAIN

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 29)

Asymmetric Unit (5, 29)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID
2CIT1Ligand/IonCITRIC ACID
3GOL5Ligand/IonGLYCEROL
4GSH1Ligand/IonGLUTATHIONE
5MSE21Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (3, 11)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID
2CIT-1Ligand/IonCITRIC ACID
3GOL3Ligand/IonGLYCEROL
4GSH-1Ligand/IonGLUTATHIONE
5MSE7Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (3, 9)
No.NameCountTypeFull Name
1ACY-1Ligand/IonACETIC ACID
2CIT-1Ligand/IonCITRIC ACID
3GOL1Ligand/IonGLYCEROL
4GSH1Ligand/IonGLUTATHIONE
5MSE7Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (3, 9)
No.NameCountTypeFull Name
1ACY-1Ligand/IonACETIC ACID
2CIT1Ligand/IonCITRIC ACID
3GOL1Ligand/IonGLYCEROL
4GSH-1Ligand/IonGLUTATHIONE
5MSE7Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:5 , ASP A:51 , ASP A:53 , LYS A:212 , ALA A:213 , HOH A:290 , ARG C:5 , CYS C:50 , ASP C:51BINDING SITE FOR RESIDUE GOL A 261
2AC2SOFTWAREARG A:117 , SER A:121 , GLY A:122 , THR A:123 , HOH A:323BINDING SITE FOR RESIDUE GOL A 262
3AC3SOFTWAREARG A:75 , PHE A:199BINDING SITE FOR RESIDUE ACY A 263
4AC4SOFTWARELYS A:34 , TRP A:35 , HOH A:248 , LYS C:45BINDING SITE FOR RESIDUE GOL A 264
5AC5SOFTWAREARG B:5 , CYS B:50 , VAL B:52 , ASP B:53 , LYS B:212BINDING SITE FOR RESIDUE GOL B 261
6AC6SOFTWARETHR B:9 , SER B:11 , THR B:40 , HIS B:58 , PHE B:83 , ARG B:117 , GLY B:122 , THR B:123 , ASN B:198 , TYR B:200BINDING SITE FOR RESIDUE GSH B 262
7AC7SOFTWAREASN C:14 , THR C:15 , ARG C:117 , SER C:121 , GLY C:122 , THR C:123 , HOH C:255BINDING SITE FOR RESIDUE CIT C 261
8AC8SOFTWARESER C:11 , THR C:40BINDING SITE FOR RESIDUE GOL C 262

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:50 -A:210
2B:50 -B:210
3C:50 -C:210

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3KN3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3KN3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3KN3)

(-) Exons   (0, 0)

(no "Exon" information available for 3KN3)

(-) 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:237
 aligned with Q7M8V9_WOLSU | Q7M8V9 from UniProtKB/TrEMBL  Length:277

    Alignment length:237
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       
         Q7M8V9_WOLSU    25 AAELRMATTTSTDNTGLLDVLAPAYKKDTGVDLKWVAVGTGNALKLGENCDVDVVFVHAPKVELEYVEKGFGIDRTPVMYNDFVIIGNPSFKQKFTGMSVAEAFKLIEKEQVKFVSRGDKSGTHSKEREVWKEALGKIPEKESWYIEAGQGMLATINIAEEQKGLTLTDRGTFIKYESNHKGKPPMVIVLEGDNTLKNFYSIMAVNPKRCEKADYKGAKQFIDWIVSEKMQAEIANF 261
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeehhhhhhhhhhhhhhhhhhhhh.eeeeeeehhhhhhhhhhh....eeee.hhhhhhhhhhhh.eeeeeeee...eeeee..hhhhhhh..hhhhhhhhhhhhh..eee....hhhhhhhhhhhhhhhh........eee...hhhhhhhhhhhh..eeeeehhhhhhhhhhh......eeee..hhhhh.eeeeeee........hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kn3 A   1 AAELRmATTTSTDNTGLLDVLAPAYKKDTGVDLKWVAVGTGNALKLGENCDVDVVFVHAPKVELEYVEKGFGIDRTPVmYNDFVIIGNPSFKQKFTGmSVAEAFKLIEKEQVKFVSRGDKSGTHSKEREVWKEALGKIPEKESWYIEAGQGmLATINIAEEQKGLTLTDRGTFIKYESNHKGKPPmVIVLEGDNTLKNFYSImAVNPKRCEKADYKGAKQFIDWIVSEKmQAEIANF 237
                                 |  10        20        30        40        50        60        70        80        90       100       110       120       130       140       150 |     160       170       180     | 190       200  |    210       220       230       
                                 6-MSE                                                                   79-MSE             98-MSE                                               152-MSE                           186-MSE          203-MSE                    230-MSE   


Chain B from PDB  Type:PROTEIN  Length:238
 aligned with Q7M8V9_WOLSU | Q7M8V9 from UniProtKB/TrEMBL  Length:277

    Alignment length:238
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255        
         Q7M8V9_WOLSU    26 AELRMATTTSTDNTGLLDVLAPAYKKDTGVDLKWVAVGTGNALKLGENCDVDVVFVHAPKVELEYVEKGFGIDRTPVMYNDFVIIGNPSFKQKFTGMSVAEAFKLIEKEQVKFVSRGDKSGTHSKEREVWKEALGKIPEKESWYIEAGQGMLATINIAEEQKGLTLTDRGTFIKYESNHKGKPPMVIVLEGDNTLKNFYSIMAVNPKRCEKADYKGAKQFIDWIVSEKMQAEIANFKL 263
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeehhhhh.hhhhhhhhhhhhhhh.eeeeeeehhhhhhhhhhh....eeee.hhhhhhhhhhh..eeeeeeee...eeeeehhhhh......hhhhhhhhhhhhh..eee....hhhhhhhhhhhhhhhh........eee...hhhhhhhhhhhh..eeeeehhhhhhhhhh.......eeee..hhhhh.eeeeeee........hhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kn3 B   2 AELRmATTTSTDNTGLLDVLAPAYKKDTGVDLKWVAVGTGNALKLGENCDVDVVFVHAPKVELEYVEKGFGIDRTPVmYNDFVIIGNPSFKQKFTGmSVAEAFKLIEKEQVKFVSRGDKSGTHSKEREVWKEALGKIPEKESWYIEAGQGmLATINIAEEQKGLTLTDRGTFIKYESNHKGKPPmVIVLEGDNTLKNFYSImAVNPKRCEKADYKGAKQFIDWIVSEKmQAEIANFKL 239
                                |   11        21        31        41        51        61        71       |81        91      |101       111       121       131       141       151|      161       171       181    |  191       201 |     211       221       231        
                                6-MSE                                                                   79-MSE             98-MSE                                               152-MSE                           186-MSE          203-MSE                    230-MSE     


Chain C from PDB  Type:PROTEIN  Length:237
 aligned with Q7M8V9_WOLSU | Q7M8V9 from UniProtKB/TrEMBL  Length:277

    Alignment length:237
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       
         Q7M8V9_WOLSU    26 AELRMATTTSTDNTGLLDVLAPAYKKDTGVDLKWVAVGTGNALKLGENCDVDVVFVHAPKVELEYVEKGFGIDRTPVMYNDFVIIGNPSFKQKFTGMSVAEAFKLIEKEQVKFVSRGDKSGTHSKEREVWKEALGKIPEKESWYIEAGQGMLATINIAEEQKGLTLTDRGTFIKYESNHKGKPPMVIVLEGDNTLKNFYSIMAVNPKRCEKADYKGAKQFIDWIVSEKMQAEIANFK 262
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) PBP_like_2-3kn3C01 C:2-229                                                                                                                                                                                                          --------- Pfam domains (1)
           Pfam domains (2) PBP_like_2-3kn3C02 C:2-229                                                                                                                                                                                                          --------- Pfam domains (2)
           Pfam domains (3) PBP_like_2-3kn3C03 C:2-229                                                                                                                                                                                                          --------- Pfam domains (3)
         Sec.struct. author .eeeeeeehhhhhhhhhhhhhhhhhhhhh.eeeeeeehhhhhhhhhhh....eeee.hhhhhhhhhhh..eeeeeeeeeeeeeeeehhhhh......hhhhhhhhhhhh...eee....hhhhhhhhhhhhhhhh........eee...hhhhhhhhhhhh...eeeehhhhhhhhhh.......eeee..hhh.eeeeeeeee........hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kn3 C   2 AELRmATTTSTDNTGLLDVLAPAYKKDTGVDLKWVAVGTGNALKLGENCDVDVVFVHAPKVELEYVEKGFGIDRTPVmYNDFVIIGNPSFKQKFTGmSVAEAFKLIEKEQVKFVSRGDKSGTHSKEREVWKEALGKIPEKESWYIEAGQGmLATINIAEEQKGLTLTDRGTFIKYESNHKGKPPmVIVLEGDNTLKNFYSImAVNPKRCEKADYKGAKQFIDWIVSEKmQAEIANFK 238
                                |   11        21        31        41        51        61        71       |81        91      |101       111       121       131       141       151|      161       171       181    |  191       201 |     211       221       231       
                                6-MSE                                                                   79-MSE             98-MSE                                               152-MSE                           186-MSE          203-MSE                    230-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 3KN3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3KN3)

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: PBP (391)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3KN3)

 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
    ACY  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CIT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GSH  [ 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 ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3kn3)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ 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 | 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)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3kn3
    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
  Q7M8V9_WOLSU | Q7M8V9
    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
  Q7M8V9_WOLSU | Q7M8V9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3KN3)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3KN3)