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

(-) Description

Title :  STRUCTURE OF CPF1/RNA COMPLEX
 
Authors :  D. Dong, K. Ren, X. Qiu, J. Wang, Z. Huang
Date :  24 Feb 16  (Deposition) - 27 Apr 16  (Release) - 11 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.38
Chains :  Asym./Biol. Unit :  A,G
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Dong, K. Ren, X. Qiu, J. Zheng, M. Guo, X. Guan, H. Liu, N. Li, B. Zhang, D. Yang, C. Ma, S. Wang, D. Wu, Y. Ma, S. Fan, J. Wang, N. Gao, Z. Huang
The Crystal Structure Of Cpf1 In Complex With Crispr Rna
Nature V. 532 522 2016
PubMed-ID: 27096363  |  Reference-DOI: 10.1038/NATURE17944

(-) Compounds

Molecule 1 - CPF1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Organism ScientificLACHNOSPIRACEAE BACTERIUM ND2006
    Organism Taxid1410628
 
Molecule 2 - RNA (5'- R(P*AP*AP*UP*UP*UP*CP*UP*AP*CP*UP*AP*AP*GP*UP*GP*UP*AP*GP*AP*UP*C)- 3')
    ChainsG
    EngineeredYES
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AG

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 21)

Asymmetric/Biological Unit (2, 21)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2MSE19Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:716 , A G:19binding site for residue MG A 1301
2AC2SOFTWAREHOH G:201 , HOH G:202 , HOH G:203 , HOH G:204 , HOH G:205 , HOH G:206binding site for residue MG G 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5ID6)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Asn A:142 -Ser A:143
2Gly A:477 -Lys A:478
3Asn A:607 -Pro A:608
4Gly A:734 -Gln A:735
5Gly A:1109 -Asp A:1110

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5ID6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5ID6)

(-) Exons   (0, 0)

(no "Exon" information available for 5ID6)

(-) Sequences/Alignments

Asymmetric/Biological 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:1209
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh.....eeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh...hhhhhh....hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhee.......eehhhhhhhhhhhh...................hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eee.hhhhhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh.eeehhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eee..............hhhhhheeeeee..eeeeeee.hhhhhhhh.........eeeee......hhhhhhhhhhh..hhhhhh..hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh.hhhhhhhhhhhhh....eeeeehhhhhhhhhh..eeeeeeehhhhh.......hhhhhhhhhh........eee....eeeee....hhhhh.ee.....ee.........ee.....ee.hhhhhh.eeeeeeeeee........hhhhhhhhhhhh.....eeeeee.....eeeeee.....eeeeee..eeeeee..eeeeeehhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.............hhhhhhhhhhhhhhhhhh................................ee..eeee.......................hhhhhhhhhhhh.eeeee....eeeeeee.hhh.........eeee....eeee.......eeeehhhhhhhhhhhhh.......hhhhhhh..hhhhhhhhhhhhhhhhh.eee.......eeeeeeee.....eee..............hhhhhhhhhhhhhhhhhhhhhh.....hhhhh....hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5id6 A    0 AASKLEKFTNCYSLSKTLRFKAIPVGKTQENIDNKRLLVEDEKRAEDYKGVKKLLDRYYLSFINDVLHSIKLKNLNNYISLFRKKTRTEKENKELENLEINLRKEIAKAFKGAAGYKSLFKKDIIETILPEAAKDEIALVNSFNGFTTAFTGFFDNRENmFSEEAKSTSIAFRCINENLTRYISNmDIFEKVDAIFDKHEVQEIKEKILNSDYDVEDFFEGEFFNFVLTQEGIDVYNAIIGGFVTESGEKIKGLNEYINLYNAKTKQALPKFKPLYKQVEGYTSDEEVLEVFRNTLNKNSEIFSSIKKLEKLFKNFDEYSSAGIFVKNGPAISTISKDIFGEWNLIRDKWNAEYDDIHLKKKAVVTEKYEDDRRKSFKKIGSFSLEQLQEYADADLSVVEKLKEIIIQKVDEIYKVYGSSEKLFDADFVLEKSLKKNDAVVAImKDLLDSVKSFENYIKAFFGEGKETNRDESFYGDFVLAYDILLKVDHIYDAIRNYVTQKPYSKDKFKLYFQNPQFmGGWDKDKETDYRATILRYGSKYYLAImDKKYAKCLQKIDKDDVNGNYEKINYKLLPGPNKmLPKVFFSKKWmAYYNPSEDIQKIYKNGTFKKGDmFNLNDCHKLIDFFKDSISRYPKWSNAYDFNFSETEKYKDIAGFYREVEEQGYKVSFESASKKEVDKLVEEGKLYmFQIYNKDFSDKSHGTPNLHTmYFKLLFDENNHGQIRLSGGAELFmRRASLKKEELVVHPANSPIANKNPDNPKKTTTLSYDVYKDKRFSEDQYELHIPIAINKCPKNIFKINTEVRVLLKHDDNPYVIGIDRGERNLLYIVVVDGKGNIVEQYSLNEIINNFNGIRIKTDYHSLLDKKEKERFEARQNWTSIENIKELKAGYISQVVHKICELVEKYDAVIALEDLNSGFKNSRVKVEKQVYQKFEKmLIDKLNYmVDKKSNPCATGGALKGYQITNKFESFKSmSTQNGFIFYIPAWLTSKIDPSTGFVNLLKTKYTSIADSKKFISSFDRImYVPEEDLFEFALDYKNFSRTDADYIKKWKLYSYGNRIRIFAAAAWEEVCLTSAYKELFNKYGINYQQGDIRALLCEQSDKAFYSSFmALmSLmLQmRNSITGRTDVDFLISPVKNSDGIFYDSRNYEAQENAILPKNADANGAYNIARKVLWAIGQFKKAEDEKLDKVKIAISNKEWLEYAQTSVK 1227
                                     9        19        29        39        49        59        69        79        89        99       109       119       129  ||   141       151       161       171       181     | 191       201       211       221       231       241       251       261       271       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452   |   462       472       482       492       502       512       522       532       542       552     | 562       572       582       592       602|      612       622   |   632       642       652       662       672       682       692       702       712       722       732       742   |   752       762       772       782       792       802       812       822       832       842       852       862       872       882       892       902       912       922       932       942      |952    |  962       972       982   |   992      1002      1012      1022      1032  |   1042      1052      1062      1072     |1088      1098      1108      1118      1128  |  |1138      1148      1158      1168      1178      1188      1198      1208      1218         
                                                                                                                                                              132|                       161-MSE                   187-MSE                                                                                      280|                                                                                                                                                                 456-MSE                                                                    531-MSE                    558-MSE                           592-MSE    603-MSE                626-MSE                                                                    701-MSE              722-MSE                 746-MSE                                                                                                                                                                                                    949-MSE 957-MSE                      986-MSE                                         1035-MSE                                   1078|                                       1128-MSE |  |                                                                                          
                                                                                                                                                               135                                                                                                                                               292                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               1085                                          1131-MSE |                                                                                          
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    1134-MSE                                                                                         
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       1137-MSE                                                                                      

Chain G from PDB  Type:RNA  Length:21
                                                      
                5id6 G    3 AAUUUCUACUAAGUGUAGAUC   23
                                    12        22 

   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 5ID6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5ID6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5ID6)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5ID6)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asn A:142 - Ser A:143   [ RasMol ]  
    Asn A:607 - Pro A:608   [ RasMol ]  
    Gly A:1109 - Asp A:1110   [ RasMol ]  
    Gly A:477 - Lys A:478   [ RasMol ]  
    Gly A:734 - Gln A:735   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5id6
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  A0A182DWE3_9 | A0A182DWE3
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  A0A182DWE3_9 | A0A182DWE3
    Protein Disorder PredictionDisEMBL | 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 5ID6)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5ID6)