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 :  TOPOISOMERASE II-DNA-AMPPNP COMPLEX
 
Authors :  B. H. Schmidt, N. Osheroff, J. M. Berger
Date :  03 Aug 12  (Deposition) - 03 Oct 12  (Release) - 12 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.41
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H,I,J
Keywords :  Topoisomerase, Protein-Dna Complex, Dna Supercoiling, Dna Replication, Atp-Binding, Dna-Binding, Isomerase, Nucleotide- Binding, Nucleus, Phosphoprotein, Isomerase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. H. Schmidt, N. Osheroff, J. M. Berger
Structure Of A Topoisomerase Ii-Dna-Nucleotide Complex Reveals A New Control Mechanism For Atpase Activity.
Nat. Struct. Mol. Biol. V. 19 1147 2012
PubMed-ID: 23022727  |  Reference-DOI: 10.1038/NSMB.2388

(-) Compounds

Molecule 1 - DNA TOPOISOMERASE 2
    Chains: A, F
    EC Number: 5.99.1.3
    Engineered: YES
    Fragment: UNP RESIDUES 1-1177
    Gene: TOP2, TOR3, YNL088W, N2244
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: DNA TOPOISOMERASE II
 
Molecule 2 - DNA (5'-D(P*CP*CP*TP*AP*CP*TP*GP*CP*TP*AP*C)-3')
    Chains: B, G
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*CP*GP*CP*GP*GP*TP*AP*GP*CP*AP*GP*TP*AP*GP*G)- 3')
    Chains: C, H
    Engineered: YES
    Synthetic: YES
 
Molecule 4 - DNA (5'-D(P*GP*GP*AP*TP*GP*AP*CP*GP*AP*TP*(TSP))-3')
    Chains: D, I
    Engineered: YES
    Synthetic: YES
 
Molecule 5 - DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*CP*GP*TP*CP*AP*TP*CP*C)- 3')
    Chains: E, J
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric/Biological Unit : ABCDEFGHIJ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1ANP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2MG2Ligand/IonMAGNESIUM ION
3PTR2Mod. Amino AcidO-PHOSPHOTYROSINE
4TSP2Mod. Nucleotide3'-THIO-THYMIDINE-5'-PHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:66 , ASN A:70 , ANP A:1202BINDING SITE FOR RESIDUE MG A 1201
2AC2SOFTWAREASN A:70 , ASN A:74 , ARG A:77 , ASN A:99 , ILE A:104 , ILE A:120 , PHE A:121 , THR A:126 , SER A:127 , SER A:128 , ASN A:129 , GLY A:140 , ARG A:141 , ASN A:142 , GLY A:143 , TYR A:144 , GLY A:145 , ALA A:146 , LYS A:147 , THR A:195 , GLN A:365 , LYS A:367 , MG A:1201BINDING SITE FOR RESIDUE ANP A 1202
3AC3SOFTWAREGLU F:66 , ASN F:70 , ANP F:1202BINDING SITE FOR RESIDUE MG F 1201
4AC4SOFTWAREASN F:70 , ASN F:74 , ARG F:77 , ASN F:99 , ILE F:104 , ILE F:120 , PHE F:121 , THR F:126 , SER F:127 , SER F:128 , ASN F:129 , GLY F:140 , ARG F:141 , ASN F:142 , GLY F:143 , TYR F:144 , GLY F:145 , ALA F:146 , LYS F:147 , THR F:195 , GLN F:365 , LYS F:367 , MG F:1201BINDING SITE FOR RESIDUE ANP F 1202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4GFH)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4GFH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GFH)

(-) 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:1103
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhee.hhhhhhhhhhhhh......eeeeeeeee....eeeeeeeeehhhhhhhhhhhhhhhhhhhhhh....eeeeeee....eeeeee...............hhhhhhhhh..ee................hhhhhhhhheeeeeeeeee....eeeeeeee....ee...eeee.......eeeeeeehhhhhh....hhhhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhh.......eeeeee..eeeeeee.....eeeeee...ee..eehhhhhhhhhhhhhhhhhhhhhh....hhhhhhh.eeeeeee.............ee..hhhhh......hhhhhhhhh.hhhhhhhhhhhh..........................eeeeeehhhhhhhhhhhhhhhh...eeeeee..........hhhhhhhhhhhhhhhhhh.........hhhhh...eeeee...hhhhhhhhhhhhhhhhhhh.........eeee....eeeee......eeee.hhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhh....eeeee.....hhhhhhhhhh..hhhhhhhhhhhh...........eeehhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh.....eehhhhhhhhhhhh....hhhhhhhhhhhhhh..................................ee....hhhhhhhhhhh....eeee..eeeee..............eeee....eeee...hhhhhhhhhhhhhh................eeee.....eeee.eeeeee..eeeeee.....hhhhhhhhhhhhhhh.........eeee.......eeee.hhhhhhhhhhhhhhhhh..eeee.....eee.....eee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh...ee.....ee.........hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4gfh A    7 SASDKYQKISQLEHILKRPDTYIGSVETQEQLQWIYDEETDCMIEKNVTIVPGLFKIFDEILVNAADNKVRDPSMKRIDVNIHAEEHTIEVKNDGKGIPIEIHNKENIYIPEMIFGHLLTSSNYDDDEKKVTGGRNGYGAKLCNIFSTEFILETADLNVGQKYVQKWENNMSICHPPKITSYKKGPSYTKVTFKPDLTRFGMKELDNDILGVMRRRVYDINGSVRDINVYLNGKSLKIRNFKNYVELYLKSLIPTILYERINNRWEVAFAVSDISFQQISFVNSIATTMGGTHVNYITDQIVKKISEILKKKKKKSVKSFQIKNNMFIFINCLIENPAFTSQTKEQLTTRVKDFGSRCEIPLEYINKIMKTDLATRMFEIADANESRITNYPKLEDANKAGTKEGYKCTLVLTEGDSALSLAVAGLAVVGRDYYGCYPLRGKMLNVREASADQILKNAEIQAIKKIMGLQHRKKYEDTKSLRYGHLMIMTDQDHDGSHIKGLIINFLESSFPGLLDIQGFLLEFITPIIKVSITKPTKNTIAFYNMPDYEKWREEESHKFTWKQKYYTSLAQEVREYFSNLDRHLKIFHSLQGNDKDYIDLAFSKKKADDRKEWLRQYEPGTVLDPTLKEIPISDFINKELILFSLADNIRSIPNVLDGFKPGQRKVLYGCFKKNLKSELKVAQLAPYVSECTAYHHGEQSLAQTIIGLAQNFVGSNNIYLLLPNGAFGTRATGGKDAAAARyYIYTELNKLTRKIFHPADDPLYKYIQEDEKTVEPEWYLPILPMILVNGAEGIGTGWSTYIPPFNPLEIIKNIRHLMNDEELEQMHPWFRGWTGTIEEIEPLRYRMYGRIEQIGDNVLEITELPARTWTSTIKEYLLLGLSGNDKIKPWIKDMEEQHDDNIKFIITLSPEEMAKTRKIGFYERFKLISPISLMNMVAFDPHGKIKKYNSVNEILSEFYYVRLEYYQKRKDHMSERLQWEVEKYSFQVKFIKMIIEKELTVTNKPRNAIIQELENLGFPRFNKEGKPYYGSEELYGTYEYLLGMRIWSLTKERYQKLLKQKQEKETELENLLKLSAKDIWNTDLKAFEVGYQEFLQRDAEAR 1177
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256 ||    283       293       303       313       323       333       343       353       363       373       383       393       403    || 425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595      |609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779  |    788       798       808       818       828       838       848       858       868       878       888       898       908       918       928       938       948       958       968       978       988       998      1008      1018      1028      1038      1048      1058      1068 ||   1114      1124      1134      1144      1154      1164      1174   
                                                                                                                                                                                                                                                                                     258|                                                                                                                                 408|                                                                                                                                                                                  602|                                                                                                                                                                            782-PTR                                                                                                                                                                                                                                                                                         1070|                                                                      
                                                                                                                                                                                                                                                                                      276                                                                                                                                  421                                                                                                                                                                                   607                                                                                                                                                                                                                                                                                                                                                                                                                                                                             1107                                                                      


Chain B from PDB  Type:DNA  Length:11
                                            
                4gfh B    1 CCTACTGCTAC   11
                                    10 


Chain C from PDB  Type:DNA  Length:15
                                                
                4gfh C    1 CGCGGTAGCAGTAGG   15
                                    10     


Chain D from PDB  Type:DNA  Length:11
                                            
                4gfh D    1 GGATGACGATt   11
                                    10|
                                     11-TSP


Chain E from PDB  Type:DNA  Length:15
                                                
                4gfh E    1 CGCGAATCGTCATCC   15
                                    10     


Chain F from PDB  Type:PROTEIN  Length:1099
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhee.hhhhhhhhhhhhh......eeeeeeeee....eeeeeeeeehhhhhhhhhhhhhhhhhhhhhh....eeeeeee....eeeeee...............hhhhhhhhh..ee................hhhhhhhhheeeeeeeeee....eeeeeeee....ee...eeee.......eeeeeeehhhhhh....hhhhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhh.......eeeeee..eeeeeee.....eeeeee...ee..eehhhhhhhhhhhhhhhhhhhhhh....hhhhhhh.eeeeeee.............ee..hhhhh......hhhhhhhhh.hhhhhhhhhhh.......................eeeeeehhhhhhhhhhhhhhhh...eeeeee..........hhhhhhhhhhhhhhhhhh.........hhhhh...eeeee...hhhhhhhhhhhhhhhhhhh.........eeee....eeeee......eeee.hhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhh....eeeee.....hhhhhhhhhh..hhhhhhhhhhhh...........eeehhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh.....eehhhhhhhhhhhh....hhhhhhhhhhhhhh..................................ee....hhhhhhhhhhh....eeee..eeeee..............eeee....eeee...hhhhhhhhhhhhhh................eeee.....eeee.eeeeee..eeeeee.....hhhhhhhhhhhhhhh.........eeee.......eeee.hhhhhhhhhhhhhhhhh..eeee.....eee.....eee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh...ee.....ee.........hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4gfh F    7 SASDKYQKISQLEHILKRPDTYIGSVETQEQLQWIYDEETDCMIEKNVTIVPGLFKIFDEILVNAADNKVRDPSMKRIDVNIHAEEHTIEVKNDGKGIPIEIHNKENIYIPEMIFGHLLTSSNYDDDEKKVTGGRNGYGAKLCNIFSTEFILETADLNVGQKYVQKWENNMSICHPPKITSYKKGPSYTKVTFKPDLTRFGMKELDNDILGVMRRRVYDINGSVRDINVYLNGKSLKIRNFKNYVELYLKSLIPTILYERINNRWEVAFAVSDISFQQISFVNSIATTMGGTHVNYITDQIVKKISEILKKKKKKSVKSFQIKNNMFIFINCLIENPAFTSQTKEQLTTRVKDFGSRCEIPLEYINKIMKTDLATRMFEIASRITNYPKLEDANKAGTKEGYKCTLVLTEGDSALSLAVAGLAVVGRDYYGCYPLRGKMLNVREASADQILKNAEIQAIKKIMGLQHRKKYEDTKSLRYGHLMIMTDQDHDGSHIKGLIINFLESSFPGLLDIQGFLLEFITPIIKVSITKPTKNTIAFYNMPDYEKWREEESHKFTWKQKYYTSLAQEVREYFSNLDRHLKIFHSLQGNDKDYIDLAFSKKKADDRKEWLRQYEPGTVLDPTLKEIPISDFINKELILFSLADNIRSIPNVLDGFKPGQRKVLYGCFKKNLKSELKVAQLAPYVSECTAYHHGEQSLAQTIIGLAQNFVGSNNIYLLLPNGAFGTRATGGKDAAAARyYIYTELNKLTRKIFHPADDPLYKYIQEDEKTVEPEWYLPILPMILVNGAEGIGTGWSTYIPPFNPLEIIKNIRHLMNDEELEQMHPWFRGWTGTIEEIEPLRYRMYGRIEQIGDNVLEITELPARTWTSTIKEYLLLGLSGNDKIKPWIKDMEEQHDDNIKFIITLSPEEMAKTRKIGFYERFKLISPISLMNMVAFDPHGKIKKYNSVNEILSEFYYVRLEYYQKRKDHMSERLQWEVEKYSFQVKFIKMIIEKELTVTNKPRNAIIQELENLGFPRFNKEGKPYYGSEELYGTYEYLLGMRIWSLTKERYQKLLKQKQEKETELENLLKLSAKDIWNTDLKAFEVGYQEFLQRDAEAR 1177
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256 ||    283       293       303       313       323       333       343       353       363       373       383       393       403||     429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599  ||   613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       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      1108      1118      1128      1138      1148      1158      1168         
                                                                                                                                                                                                                                                                                     258|                                                                                                                             404|                                                                                                                                                                                  602|                                                                                                                                                                            782-PTR                                                                                                                                                                                                                                                                                         1070|                                                                      
                                                                                                                                                                                                                                                                                      276                                                                                                                              421                                                                                                                                                                                   607                                                                                                                                                                                                                                                                                                                                                                                                                                                                             1107                                                                      


Chain G from PDB  Type:DNA  Length:11
                                            
                4gfh G    1 CCTACTGCTAC   11
                                    10 


Chain H from PDB  Type:DNA  Length:15
                                                
                4gfh H    1 CGCGGTAGCAGTAGG   15
                                    10     


Chain I from PDB  Type:DNA  Length:11
                                            
                4gfh I    1 GGATGACGATt   11
                                    10|
                                     11-TSP


Chain J from PDB  Type:DNA  Length:15
                                                
                4gfh J    1 CGCGAATCGTCATCC   15
                                    10
   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 4GFH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (25, 25)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    ANP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PTR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TSP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4gfh)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - 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
  4gfh
    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
  TOP2_YEAST | P06786
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  5.99.1.3
    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
  TOP2_YEAST | P06786
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        TOP2_YEAST | P06786: 1bgw 1bjt 1pvg 1qzr 2rgr 3l4j 3l4k

(-) Related Entries Specified in the PDB File

1pvg YEAST ATPASE
3l4j YEAST DNA BINDING AND CLEAVAGE CORE
3l4k YEAST DNA BINDING AND CLEAVAGE CORE