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
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)

(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE GLYCOSYL HYDROLASE (NP_813087.1) FROM BACTEROIDES THETAIOTAOMICRON VPI-5482 AT 1.80 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  25 Sep 09  (Deposition) - 03 Nov 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Putative Glycosyl Hydrolase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Unknown Function, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Glycosyl Hydrolase (Np_813087. 1) From Bacteroides Thetaiotaomicron Vpi-5482 At 1. 80 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE GLYCOSYL HYDROLASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BT_4176
    Organism Scientific: BACTEROIDES THETAIOTAOMICRON VPI-5482
    Organism Taxid: 226186

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 30)

Asymmetric Unit (3, 30)
No.NameCountTypeFull Name
1EDO19Ligand/Ion1,2-ETHANEDIOL
2MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3MSE10Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (3, 90)
No.NameCountTypeFull Name
1EDO57Ligand/Ion1,2-ETHANEDIOL
2MES3Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3MSE30Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:49 , LYS A:53 , ILE A:431 , ASN A:435 , HOH A:781 , HOH A:864 , HOH A:868BINDING SITE FOR RESIDUE EDO A 1
02AC2SOFTWAREGLN A:41 , GLY A:42 , THR A:43 , GLY A:329 , GLU A:330 , TYR A:409 , HOH A:544BINDING SITE FOR RESIDUE EDO A 2
03AC3SOFTWAREEDO A:7 , ASP A:278 , HIS A:279 , ARG A:321 , HOH A:557 , HOH A:653 , HOH A:676BINDING SITE FOR RESIDUE EDO A 3
04AC4SOFTWARELYS A:311 , TYR A:315 , HOH A:581 , HOH A:733 , HOH A:809BINDING SITE FOR RESIDUE EDO A 4
05AC5SOFTWAREEDO A:12 , ASP A:300 , VAL A:301 , LEU A:302 , GLU A:304 , HOH A:599BINDING SITE FOR RESIDUE EDO A 5
06AC6SOFTWARETHR A:277 , ARG A:317 , GLY A:363 , TRP A:364 , ILE A:365 , ASP A:366 , HOH A:622BINDING SITE FOR RESIDUE EDO A 6
07AC7SOFTWAREEDO A:3 , ARG A:269 , HIS A:279 , ALA A:281 , HOH A:801BINDING SITE FOR RESIDUE EDO A 7
08AC8SOFTWAREEDO A:9 , TYR A:102 , ASP A:165 , ARG A:211 , ARG A:213 , ASP A:222 , MSE A:226BINDING SITE FOR RESIDUE EDO A 8
09AC9SOFTWAREEDO A:8 , HIS A:34 , ARG A:213 , GLY A:399 , ASP A:443BINDING SITE FOR RESIDUE EDO A 9
10BC1SOFTWAREASN A:340 , SER A:342 , HOH A:501BINDING SITE FOR RESIDUE EDO A 10
11BC2SOFTWAREASP A:341 , TYR A:409 , HOH A:494 , HOH A:863 , HOH A:877BINDING SITE FOR RESIDUE EDO A 11
12BC3SOFTWAREEDO A:5 , LYS A:242 , PRO A:303 , HOH A:722 , HOH A:741 , HOH A:914BINDING SITE FOR RESIDUE EDO A 12
13BC4SOFTWAREGLU A:264 , LYS A:265 , GLY A:266 , GLY A:322 , HOH A:521 , HOH A:705 , HOH A:926BINDING SITE FOR RESIDUE EDO A 13
14BC5SOFTWARELYS A:78 , TYR A:343 , LEU A:344 , VAL A:412 , HOH A:646 , HOH A:731 , HOH A:820BINDING SITE FOR RESIDUE EDO A 14
15BC6SOFTWARELEU A:179 , LYS A:180 , ASP A:181 , GLU A:182BINDING SITE FOR RESIDUE EDO A 15
16BC7SOFTWARELYS A:74 , ASP A:88 , THR A:151 , ASP A:152 , HOH A:677BINDING SITE FOR RESIDUE EDO A 16
17BC8SOFTWARETHR A:124 , GLN A:128 , HOH A:764BINDING SITE FOR RESIDUE EDO A 17
18BC9SOFTWAREGLN A:37 , TYR A:44 , MSE A:441 , HOH A:556 , HOH A:669BINDING SITE FOR RESIDUE EDO A 18
19CC1SOFTWAREGLY A:383 , ASN A:386 , GLU A:392 , HOH A:799BINDING SITE FOR RESIDUE EDO A 19
20CC2SOFTWARELYS A:454 , PHE A:460 , ALA A:461 , ASP A:463 , HOH A:487 , HOH A:719 , HOH A:746BINDING SITE FOR RESIDUE MES A 20

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3K11)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Arg A:213 -Pro A:214

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3K11)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3K11)

(-) Exons   (0, 0)

(no "Exon" information available for 3K11)

(-) 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:439
 aligned with Q8A045_BACTN | Q8A045 from UniProtKB/TrEMBL  Length:465

    Alignment length:439
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455         
         Q8A045_BACTN    26 INDSNTPLHLLQPAYQGTYGDLTPEQVKKDIDRVFAYIDKETPARVVDKNTGKVITDYTAMGDEAQLERGAFRLASYEWGVTYSALIAAAETTGDKRYTDYVQNRFRFLAEVAPHFKRVYEEKGKTDSQLLQILTPHALDDAGAVCTAMIKLRLKDESLPVDGLIQNYFDFIINKEYRLADGTFARNRPQRNTLWLDDMFMGIPAVAQMSRYDKEAKNKYLAEAVKQFLQFADRMFIPEKGLYRHGWVESSTDHPAFCWARANGWALLTACELLDVLPEDYPQRPKVMDYFRAHVRGVTALQSGEGFWHQLLDCNDSYLETSATAIYVYCLAHAINKGWIDAIAYGPVAQLGWHAVAGKINEEGQVEGTCVGTGMAFDPAFYYYRPVNVYAAHGYGPVLWAGAEMIRLLNTQHPQMNDSAVQYYQEKQKTTAPIFAVDS 464
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------Glyco_hydro_88-3k11A01 A:62-434                                                                                                                                                                                                                                                                                                                                                      ------------------------------ Pfam domains
         Sec.struct. author ......hhhhh...........hhhhhhhhhhhhhhhhhhh....eee.....ee.........eee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.................eeehhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.........eee..........hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.......ee.........eehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...................hhhhhhh......hhhhhhhhhhhhhhhhhhhhhh..eee..eee................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k11 A  26 INDSNTPLHLLQPAYQGTYGDLTPEQVKKDIDRVFAYIDKETPARVVDKNTGKVITDYTAmGDEAQLERGAFRLASYEWGVTYSALIAAAETTGDKRYTDYVQNRFRFLAEVAPHFKRVYEEKGKTDSQLLQILTPHALDDAGAVCTAmIKLRLKDESLPVDGLIQNYFDFIINKEYRLADGTFARNRPQRNTLWLDDmFmGIPAVAQmSRYDKEAKNKYLAEAVKQFLQFADRmFIPEKGLYRHGWVESSTDHPAFCWARANGWALLTACELLDVLPEDYPQRPKVmDYFRAHVRGVTALQSGEGFWHQLLDCNDSYLETSATAIYVYCLAHAINKGWIDAIAYGPVAQLGWHAVAGKINEEGQVEGTCVGTGmAFDPAFYYYRPVNVYAAHGYGPVLWAGAEmIRLLNTQHPQmNDSAVQYYQEKQKTTAPIFAVDS 464
                                    35        45        55        65        75        85|       95       105       115       125       135       145       155       165       175       185       195       205       215       225|      235       245       255    |  265       275       285       295       305       315       325       335       345       355       365       375       385       395    |  405       415       425    |  435     | 445       455         
                                                                                       86-MSE                                                                                 174-MSE                                           224-MSE   234-MSE                   260-MSE                                              313-MSE                                                                                400-MSE                       430-MSE    441-MSE                   
                                                                                                                                                                                                                                  226-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 3K11)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3K11)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: 6_Hairpin (120)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q8A045_BACTN | Q8A045)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.

 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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MES  [ 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 ]
    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 ]
    CC1  [ RasMol ]  +environment [ RasMol ]
    CC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Arg A:213 - Pro A:214   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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 ](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
  3k11
    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
  Q8A045_BACTN | Q8A045
    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
  Q8A045_BACTN | Q8A045
    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 3K11)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3K11)