2PYJ
Phi29 DNA polymerase complexed with primer-template DNA and incoming nucleotide substrates (ternary complex)
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000166 | molecular_function | nucleotide binding |
| A | 0001882 | molecular_function | nucleoside binding |
| A | 0003676 | molecular_function | nucleic acid binding |
| A | 0003677 | molecular_function | DNA binding |
| A | 0003887 | molecular_function | DNA-directed DNA polymerase activity |
| A | 0004518 | molecular_function | nuclease activity |
| A | 0004527 | molecular_function | exonuclease activity |
| A | 0006260 | biological_process | DNA replication |
| A | 0016740 | molecular_function | transferase activity |
| A | 0016779 | molecular_function | nucleotidyltransferase activity |
| A | 0016787 | molecular_function | hydrolase activity |
| A | 0034061 | molecular_function | DNA polymerase activity |
| A | 0039693 | biological_process | viral DNA genome replication |
| A | 0046872 | molecular_function | metal ion binding |
| B | 0000166 | molecular_function | nucleotide binding |
| B | 0001882 | molecular_function | nucleoside binding |
| B | 0003676 | molecular_function | nucleic acid binding |
| B | 0003677 | molecular_function | DNA binding |
| B | 0003887 | molecular_function | DNA-directed DNA polymerase activity |
| B | 0004518 | molecular_function | nuclease activity |
| B | 0004527 | molecular_function | exonuclease activity |
| B | 0006260 | biological_process | DNA replication |
| B | 0016740 | molecular_function | transferase activity |
| B | 0016779 | molecular_function | nucleotidyltransferase activity |
| B | 0016787 | molecular_function | hydrolase activity |
| B | 0034061 | molecular_function | DNA polymerase activity |
| B | 0039693 | biological_process | viral DNA genome replication |
| B | 0046872 | molecular_function | metal ion binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MN B 9001 |
| Chain | Residue |
| B | ASP249 |
| B | VAL250 |
| B | ASP458 |
| B | DGT1589 |
| B | MG9002 |
| site_id | AC2 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE MG B 9002 |
| Chain | Residue |
| B | HOH9084 |
| B | HOH9130 |
| Q | DOC10 |
| B | ASP249 |
| B | ASP458 |
| B | DGT1589 |
| B | MN9001 |
| site_id | AC3 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MN A 9003 |
| Chain | Residue |
| A | ASP249 |
| A | VAL250 |
| A | ASP458 |
| A | DGT1588 |
| A | MG9004 |
| site_id | AC4 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE MG A 9004 |
| Chain | Residue |
| A | ASP249 |
| A | ASP458 |
| A | DGT1588 |
| A | MN9003 |
| A | HOH9158 |
| A | HOH9326 |
| X | DOC10 |
| site_id | AC5 |
| Number of Residues | 23 |
| Details | BINDING SITE FOR RESIDUE DGT A 1588 |
| Chain | Residue |
| A | ASP249 |
| A | VAL250 |
| A | ASN251 |
| A | SER252 |
| A | LEU253 |
| A | TYR254 |
| A | LYS371 |
| A | LYS383 |
| A | ASN387 |
| A | TYR390 |
| A | ASP458 |
| A | MN9003 |
| A | MG9004 |
| A | HOH9018 |
| A | HOH9042 |
| A | HOH9090 |
| A | HOH9155 |
| A | HOH9236 |
| A | HOH9326 |
| A | HOH9435 |
| X | DOC10 |
| Y | DC6 |
| Y | DG7 |
| site_id | AC6 |
| Number of Residues | 25 |
| Details | BINDING SITE FOR RESIDUE DGT B 1589 |
| Chain | Residue |
| B | ASP249 |
| B | VAL250 |
| B | ASN251 |
| B | SER252 |
| B | LEU253 |
| B | TYR254 |
| B | LYS371 |
| B | LYS383 |
| B | ASN387 |
| B | TYR390 |
| B | THR457 |
| B | ASP458 |
| B | EDO2775 |
| B | MN9001 |
| B | MG9002 |
| B | HOH9013 |
| B | HOH9017 |
| B | HOH9047 |
| B | HOH9048 |
| B | HOH9065 |
| B | HOH9130 |
| B | HOH9150 |
| Q | DOC10 |
| R | DC6 |
| R | DG7 |
| site_id | AC7 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO B 2762 |
| Chain | Residue |
| B | ARG491 |
| B | ASP503 |
| B | THR542 |
| B | PHE543 |
| B | HOH9125 |
| site_id | AC8 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO B 2763 |
| Chain | Residue |
| B | ILE504 |
| B | MET506 |
| B | GLU515 |
| B | LYS525 |
| B | HOH9266 |
| site_id | AC9 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE EDO B 2764 |
| Chain | Residue |
| B | TYR265 |
| B | THR356 |
| site_id | BC1 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO K 2765 |
| Chain | Residue |
| K | DA6 |
| K | DA10 |
| K | HOH1218 |
| site_id | BC2 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO K 2766 |
| Chain | Residue |
| K | DA6 |
| K | EDO2767 |
| R | DC4 |
| site_id | BC3 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE EDO K 2767 |
| Chain | Residue |
| B | ASP104 |
| B | LYS114 |
| B | HIS116 |
| K | DC5 |
| K | DA6 |
| K | EDO2766 |
| R | DC4 |
| site_id | BC4 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE EDO B 2769 |
| Chain | Residue |
| B | THR372 |
| B | LYS478 |
| B | LYS479 |
| B | LEU480 |
| B | HOH9026 |
| B | HOH9217 |
| B | HOH9296 |
| A | PHE309 |
| B | THR368 |
| site_id | BC5 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE EDO A 2770 |
| Chain | Residue |
| A | GLY481 |
| A | TYR482 |
| site_id | BC6 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO A 2771 |
| Chain | Residue |
| A | LYS274 |
| A | HIS284 |
| A | GLN286 |
| A | LEU333 |
| A | LYS337 |
| A | TYR347 |
| site_id | BC7 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO Y 2772 |
| Chain | Residue |
| A | LYS305 |
| Y | DA9 |
| Y | HOH1029 |
| Y | HOH1030 |
| site_id | BC8 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO A 2773 |
| Chain | Residue |
| A | ARG308 |
| A | EDO2774 |
| B | ASP365 |
| site_id | BC9 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO A 2774 |
| Chain | Residue |
| A | EDO2773 |
| A | HOH9397 |
| B | TYR369 |
| site_id | CC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO B 2775 |
| Chain | Residue |
| B | ASN251 |
| B | LYS371 |
| B | LYS379 |
| B | PRO477 |
| B | DGT1589 |
| B | HOH9008 |
| site_id | CC2 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE EDO B 2776 |
| Chain | Residue |
| B | GLY376 |
| B | LYS379 |
| site_id | CC3 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE EDO B 2777 |
| Chain | Residue |
| A | HIS149 |
| A | LYS150 |
| A | GLU151 |
| B | GLU334 |
| B | GLU338 |
| B | TRP436 |
| B | TYR439 |
| site_id | CC4 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE EDO B 2778 |
| Chain | Residue |
| B | ARG227 |
| B | THR301 |
| B | ILE302 |
| B | GLN303 |
| B | ASP332 |
| B | ARG438 |
| B | HOH9097 |
| B | HOH9122 |
| site_id | CC5 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO B 2779 |
| Chain | Residue |
| A | GLU151 |
| A | PRO153 |
| B | PRO282 |
| B | HOH9287 |
| site_id | CC6 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO A 2780 |
| Chain | Residue |
| A | ASN62 |
| A | PRO558 |
| A | HOH9262 |
| site_id | CC7 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO A 2781 |
| Chain | Residue |
| A | ASN62 |
| A | PRO129 |
| A | HOH9245 |
| site_id | CC8 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO X 2782 |
| Chain | Residue |
| A | PHE414 |
| A | ARG415 |
| A | LEU416 |
| X | DT4 |
| X | DG5 |
| X | HOH834 |
| site_id | CC9 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO A 2784 |
| Chain | Residue |
| A | LYS206 |
| A | LEU359 |
| A | HOH9377 |
| site_id | DC1 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE EDO Q 2785 |
| Chain | Residue |
| Q | DT8 |
| Q | DA9 |
| Q | DOC10 |
| Q | HOH2791 |
| Q | HOH2796 |
| Q | HOH2799 |
| Q | HOH2800 |
| site_id | DC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO A 2786 |
| Chain | Residue |
| A | GLN380 |
| A | LYS383 |
| A | HOH9229 |
| A | HOH9317 |
| site_id | DC3 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO B 2787 |
| Chain | Residue |
| B | MET4 |
| B | GLU291 |
| B | HOH9324 |
| site_id | DC4 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE EDO Y 2788 |
| Chain | Residue |
| Y | DG14 |
| site_id | DC5 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO B 2789 |
| Chain | Residue |
| A | SER551 |
| B | GLU33 |
| B | LYS182 |
| B | GLU296 |
| B | HOH9277 |
| site_id | DC6 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO A 2790 |
| Chain | Residue |
| A | ARG552 |
| A | MET554 |
| A | EDO2803 |
| B | ASP34 |
| B | GLU296 |
| site_id | DC7 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO B 2791 |
| Chain | Residue |
| B | TYR29 |
| B | SER36 |
| B | TYR38 |
| site_id | DC8 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO A 2792 |
| Chain | Residue |
| A | LYS143 |
| A | ILE323 |
| A | HOH9123 |
| A | HOH9291 |
| site_id | DC9 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE EDO A 2793 |
| Chain | Residue |
| A | GLN183 |
| A | LYS366 |
| site_id | EC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO A 2794 |
| Chain | Residue |
| A | GLN257 |
| A | THR440 |
| A | GLY481 |
| A | HOH9110 |
| A | HOH9142 |
| site_id | EC2 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE EDO B 2795 |
| Chain | Residue |
| B | HOH9202 |
| site_id | EC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO R 2796 |
| Chain | Residue |
| B | ARG496 |
| B | LYS575 |
| R | DG11 |
| R | DC12 |
| site_id | EC4 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE EDO A 2797 |
| Chain | Residue |
| A | LYS64 |
| A | GLY98 |
| A | TRP100 |
| A | LYS402 |
| A | PHE414 |
| A | HOH9197 |
| X | DG5 |
| X | DC6 |
| site_id | EC5 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO X 2798 |
| Chain | Residue |
| A | PHE414 |
| A | GLN560 |
| A | HOH9306 |
| X | DG5 |
| X | DC6 |
| X | HOH1053 |
| site_id | EC6 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO A 2800 |
| Chain | Residue |
| A | LYS64 |
| A | MET97 |
| X | DC6 |
| X | DT7 |
| site_id | EC7 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO A 2801 |
| Chain | Residue |
| A | GLY41 |
| A | ASN42 |
| A | GLU46 |
| site_id | EC8 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO B 2802 |
| Chain | Residue |
| A | PHE309 |
| A | TYR310 |
| A | SER319 |
| A | GLY320 |
| B | THR372 |
| B | LYS478 |
| site_id | EC9 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE EDO A 2803 |
| Chain | Residue |
| A | GLY549 |
| A | PHE550 |
| A | SER551 |
| A | ARG552 |
| A | EDO2790 |
| A | HOH9198 |
| B | GLU33 |
| B | ASP34 |
| B | HIS35 |
| site_id | FC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO A 2804 |
| Chain | Residue |
| A | THR92 |
| A | ILE93 |
| A | ILE94 |
| A | GLY401 |
| A | LYS402 |
| A | HOH9271 |
| site_id | FC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO B 2805 |
| Chain | Residue |
| A | LYS150 |
| B | SER260 |
| B | ARG261 |
| B | HOH9037 |
Functional Information from PROSITE/UniProt
| site_id | PS00116 |
| Number of Residues | 9 |
| Details | DNA_POLYMERASE_B DNA polymerase family B signature. YCDTDSIHL |
| Chain | Residue | Details |
| A | TYR454-LEU462 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 74 |
| Details | Region: {"description":"Involved in DNA-binding, coordination between DNA synthesis and degradation and TP interaction","evidences":[{"source":"PubMed","id":"15777661","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8670845","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9931249","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 44 |
| Details | Region: {"description":"TPR2","evidences":[{"source":"PubMed","id":"15845765","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 24 |
| Details | Region: {"description":"Involved in DNA-binding and TP interaction","evidences":[{"source":"PubMed","id":"14729920","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 8 |
| Details | Motif: {"description":"YCDTD","evidences":[{"source":"PubMed","id":"1850426","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 4 |
| Details | Binding site: {"evidences":[{"source":"PDB","id":"1XI1","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 2 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"8226957","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2PYJ","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"19883660","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2PYJ","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI8 |
| Number of Residues | 6 |
| Details | Binding site: {"evidences":[{"source":"PDB","id":"2PYL","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI9 |
| Number of Residues | 2 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"9784372","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI10 |
| Number of Residues | 2 |
| Details | Binding site: {"evidences":[{"source":"PDB","id":"2PYJ","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI11 |
| Number of Residues | 6 |
| Details | Site: {"description":"Essential for 3'-5' exonucleolysis","evidences":[{"source":"PubMed","id":"2790959","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8344956","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI12 |
| Number of Residues | 4 |
| Details | Site: {"description":"Involved in proofreading function by stabilization of the frayed primer-terminus at the 3'-5' exonuclease active site","evidences":[{"source":"PubMed","id":"8605889","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI13 |
| Number of Residues | 6 |
| Details | Site: {"description":"Interaction with the primer terminal protein","evidences":[{"source":"PubMed","id":"11884636","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI14 |
| Number of Residues | 6 |
| Details | Site: {"description":"Binds ssDNA; Essential for 3'-5' exonucleolysis","evidences":[{"source":"PubMed","id":"9786901","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI15 |
| Number of Residues | 2 |
| Details | Site: {"description":"Involved in binding template-primer structures","evidences":[{"source":"PubMed","id":"8344956","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI16 |
| Number of Residues | 2 |
| Details | Site: {"description":"Involved in the stabilization of the frayed 3' terminus at the exonuclease active site","evidences":[{"source":"PubMed","id":"19576228","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI17 |
| Number of Residues | 2 |
| Details | Site: {"description":"Probably involved in binding template-primer structures","evidences":[{"source":"PubMed","id":"8226957","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI18 |
| Number of Residues | 4 |
| Details | Site: {"description":"Probably involved in nucleotide binding selection","evidences":[{"source":"PubMed","id":"8537389","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI19 |
| Number of Residues | 4 |
| Details | Site: {"description":"Binds ssDNA; Essential for 3'-5' exonucleolysis","evidences":[{"source":"PubMed","id":"8605889","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI20 |
| Number of Residues | 2 |
| Details | Site: {"description":"Involved in the binding of DNA and dNTP","evidences":[{"source":"PubMed","id":"11917008","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI21 |
| Number of Residues | 4 |
| Details | Site: {"description":"Stabilization of the incoming nucleotide","evidences":[{"source":"PubMed","id":"14672657","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI22 |
| Number of Residues | 2 |
| Details | Site: {"description":"Interacts with the phosphate groups of the incoming nucleotide","evidences":[{"source":"PubMed","id":"11917008","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI23 |
| Number of Residues | 2 |
| Details | Site: {"description":"Probably involved in nucleotide binding selection","evidences":[{"source":"PubMed","id":"9199402","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI24 |
| Number of Residues | 2 |
| Details | Site: {"description":"Probably involved in positioning the templating nucleotide at the polymerization active site and in controlling nucleotide insertion fidelity","evidences":[{"source":"PubMed","id":"12805385","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI25 |
| Number of Residues | 4 |
| Details | Site: {"description":"Probably involved in binding template-primer structures","evidences":[{"source":"PubMed","id":"8344956","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI26 |
| Number of Residues | 4 |
| Details | Site: {"description":"Probably involved in binding template-primer structures","evidences":[{"source":"PubMed","id":"7962004","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI27 |
| Number of Residues | 4 |
| Details | Site: {"description":"Probably involved in binding template-primer structures","evidences":[{"source":"PubMed","id":"7852344","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI28 |
| Number of Residues | 2 |
| Details | Site: {"description":"Stabilizes the primer-terminus at the polymerization active site and contributes to the coordination between the exonuclease and polymerazation activities","evidences":[{"source":"PubMed","id":"24023769","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
