2FCC
Crystal Structure of T4 Pyrimidine Dimer Glycosylase (T4-Pdg) Covalently Complexed with a DNA Substrate Containing Abasic Site
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000704 | molecular_function | pyrimidine dimer DNA N-glycosylase activity |
| A | 0003906 | molecular_function | DNA-(apurinic or apyrimidinic site) endonuclease activity |
| A | 0004519 | molecular_function | endonuclease activity |
| A | 0006281 | biological_process | DNA repair |
| A | 0016798 | molecular_function | hydrolase activity, acting on glycosyl bonds |
| A | 0016829 | molecular_function | lyase activity |
| A | 0033959 | molecular_function | deoxyribodipyrimidine endonucleosidase activity |
| A | 0140078 | molecular_function | class I DNA-(apurinic or apyrimidinic site) endonuclease activity |
| B | 0000704 | molecular_function | pyrimidine dimer DNA N-glycosylase activity |
| B | 0003906 | molecular_function | DNA-(apurinic or apyrimidinic site) endonuclease activity |
| B | 0004519 | molecular_function | endonuclease activity |
| B | 0006281 | biological_process | DNA repair |
| B | 0016798 | molecular_function | hydrolase activity, acting on glycosyl bonds |
| B | 0016829 | molecular_function | lyase activity |
| B | 0033959 | molecular_function | deoxyribodipyrimidine endonucleosidase activity |
| B | 0140078 | molecular_function | class I DNA-(apurinic or apyrimidinic site) endonuclease activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE SO4 A 501 |
| Chain | Residue |
| A | THR49 |
| A | PHE50 |
| A | TYR104 |
| A | PRO106 |
| A | HIS107 |
| A | SER110 |
| A | HOH1080 |
| site_id | AC2 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 A 502 |
| Chain | Residue |
| A | GLN124 |
| A | ARG117 |
| A | LYS121 |
| site_id | AC3 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE GOL B 601 |
| Chain | Residue |
| B | THR49 |
| B | PHE50 |
| B | PHE59 |
| B | TYR104 |
| B | PRO106 |
| B | HIS107 |
| B | SER110 |
| site_id | AC4 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE GOL A 602 |
| Chain | Residue |
| A | PHE66 |
| A | LYS69 |
| A | ARG70 |
| A | GLU73 |
| A | HOH1044 |
| A | HOH1088 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 2 |
| Details | ACT_SITE: Nucleophile; via amide nitrogen => ECO:0000269|PubMed:8347626, ECO:0007744|PDB:1VAS |
| Chain | Residue | Details |
| A | THR2 | |
| B | THR2 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 2 |
| Details | ACT_SITE: Proton acceptor => ECO:0000269|PubMed:8347626, ECO:0007744|PDB:1VAS |
| Chain | Residue | Details |
| A | GLU23 | |
| B | GLU23 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | SITE: Substrate binding => ECO:0000269|PubMed:1409651, ECO:0000269|PubMed:7783199 |
| Chain | Residue | Details |
| A | ARG3 | |
| B | ARG3 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 6 |
| Details | SITE: Substrate binding => ECO:0000269|PubMed:1409651 |
| Chain | Residue | Details |
| A | ARG22 | |
| A | ARG117 | |
| A | LYS121 | |
| B | ARG22 | |
| B | ARG117 | |
| B | LYS121 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | SITE: Transition state stabilizer => ECO:0007744|PDB:1VAS |
| Chain | Residue | Details |
| A | ARG26 | |
| B | ARG26 |
Catalytic Information from CSA
| site_id | CSA1 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1vas |
| Chain | Residue | Details |
| A | ARG22 | |
| A | THR2 | |
| A | GLU23 | |
| A | ARG26 |
| site_id | CSA2 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1vas |
| Chain | Residue | Details |
| B | ARG22 | |
| B | THR2 | |
| B | GLU23 | |
| B | ARG26 |
| site_id | MCSA1 |
| Number of Residues | 4 |
| Details | M-CSA 162 |
| Chain | Residue | Details |
| A | THR2 | covalently attached, electron pair acceptor, electron pair donor, hydrogen bond acceptor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor |
| A | ARG22 | electrostatic stabiliser, hydrogen bond donor |
| A | GLU23 | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| A | ARG26 | electrostatic stabiliser, hydrogen bond donor |
| site_id | MCSA2 |
| Number of Residues | 4 |
| Details | M-CSA 162 |
| Chain | Residue | Details |
| B | THR2 | covalently attached, electron pair acceptor, electron pair donor, hydrogen bond acceptor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor |
| B | ARG22 | electrostatic stabiliser, hydrogen bond donor |
| B | GLU23 | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| B | ARG26 | electrostatic stabiliser, hydrogen bond donor |
