5HML
Crystal Structure of T5 D15 Protein Co-crystallized with Metal Ions
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0003677 | molecular_function | DNA binding |
| A | 0003824 | molecular_function | catalytic activity |
| A | 0004518 | molecular_function | nuclease activity |
| A | 0004519 | molecular_function | endonuclease activity |
| A | 0004527 | molecular_function | exonuclease activity |
| A | 0004529 | molecular_function | DNA exonuclease activity |
| A | 0006260 | biological_process | DNA replication |
| A | 0008409 | molecular_function | 5'-3' exonuclease activity |
| A | 0016787 | molecular_function | hydrolase activity |
| A | 0016788 | molecular_function | hydrolase activity, acting on ester bonds |
| A | 0017108 | molecular_function | 5'-flap endonuclease activity |
| A | 0019034 | cellular_component | viral replication complex |
| A | 0019086 | biological_process | late viral transcription |
| A | 0033567 | biological_process | DNA replication, Okazaki fragment processing |
| A | 0035312 | molecular_function | 5'-3' DNA exonuclease activity |
| A | 0039693 | biological_process | viral DNA genome replication |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0048256 | molecular_function | flap endonuclease activity |
| A | 0051908 | molecular_function | double-stranded DNA 5'-3' DNA exonuclease activity |
| A | 1990238 | molecular_function | double-stranded DNA endonuclease activity |
| B | 0003677 | molecular_function | DNA binding |
| B | 0003824 | molecular_function | catalytic activity |
| B | 0004518 | molecular_function | nuclease activity |
| B | 0004519 | molecular_function | endonuclease activity |
| B | 0004527 | molecular_function | exonuclease activity |
| B | 0004529 | molecular_function | DNA exonuclease activity |
| B | 0006260 | biological_process | DNA replication |
| B | 0008409 | molecular_function | 5'-3' exonuclease activity |
| B | 0016787 | molecular_function | hydrolase activity |
| B | 0016788 | molecular_function | hydrolase activity, acting on ester bonds |
| B | 0017108 | molecular_function | 5'-flap endonuclease activity |
| B | 0019034 | cellular_component | viral replication complex |
| B | 0019086 | biological_process | late viral transcription |
| B | 0033567 | biological_process | DNA replication, Okazaki fragment processing |
| B | 0035312 | molecular_function | 5'-3' DNA exonuclease activity |
| B | 0039693 | biological_process | viral DNA genome replication |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0048256 | molecular_function | flap endonuclease activity |
| B | 0051908 | molecular_function | double-stranded DNA 5'-3' DNA exonuclease activity |
| B | 1990238 | molecular_function | double-stranded DNA endonuclease activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 6 |
| Details | binding site for residue MG A 301 |
| Chain | Residue |
| A | ASP155 |
| A | ASP204 |
| A | HOH403 |
| A | HOH484 |
| A | HOH529 |
| A | HOH552 |
| site_id | AC2 |
| Number of Residues | 1 |
| Details | binding site for residue CL A 302 |
| Chain | Residue |
| A | GLU210 |
| site_id | AC3 |
| Number of Residues | 2 |
| Details | binding site for residue CL A 303 |
| Chain | Residue |
| A | GLY213 |
| A | ARG216 |
| site_id | AC4 |
| Number of Residues | 1 |
| Details | binding site for residue CL A 304 |
| Chain | Residue |
| A | ARG93 |
| site_id | AC5 |
| Number of Residues | 4 |
| Details | binding site for residue EDO A 305 |
| Chain | Residue |
| A | ARG33 |
| A | ASN38 |
| A | SER46 |
| A | THR50 |
| site_id | AC6 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 306 |
| Chain | Residue |
| A | ARG216 |
| A | LYS241 |
| A | TYR242 |
| site_id | AC7 |
| Number of Residues | 12 |
| Details | binding site for residue B3P B 301 |
| Chain | Residue |
| A | TYR90 |
| A | ALA91 |
| A | GLN92 |
| A | ARG93 |
| A | GLU95 |
| A | HOH518 |
| B | GLU182 |
| B | HIS183 |
| B | ASN185 |
| B | ALA214 |
| B | HOH562 |
| B | HOH576 |
| site_id | AC8 |
| Number of Residues | 6 |
| Details | binding site for residue MG B 302 |
| Chain | Residue |
| B | ASP155 |
| B | ASP204 |
| B | HOH408 |
| B | HOH447 |
| B | HOH597 |
| B | HOH616 |
| site_id | AC9 |
| Number of Residues | 6 |
| Details | binding site for residue MG B 303 |
| Chain | Residue |
| B | ASP87 |
| B | HOH416 |
| B | HOH431 |
| B | HOH470 |
| B | HOH512 |
| B | HOH670 |
| site_id | AD1 |
| Number of Residues | 4 |
| Details | binding site for residue CL B 304 |
| Chain | Residue |
| A | HOH614 |
| B | GLY213 |
| B | ARG216 |
| B | HOH656 |
| site_id | AD2 |
| Number of Residues | 1 |
| Details | binding site for residue CL B 305 |
| Chain | Residue |
| B | PHE169 |
| site_id | AD3 |
| Number of Residues | 3 |
| Details | binding site for residue CL B 306 |
| Chain | Residue |
| B | LYS239 |
| B | HOH584 |
| B | HOH664 |
| site_id | AD4 |
| Number of Residues | 1 |
| Details | binding site for residue CL B 307 |
| Chain | Residue |
| B | HIS36 |
| site_id | AD5 |
| Number of Residues | 1 |
| Details | binding site for residue CL B 308 |
| Chain | Residue |
| B | ASN38 |
| site_id | AD6 |
| Number of Residues | 2 |
| Details | binding site for residue CL B 309 |
| Chain | Residue |
| B | SER45 |
| B | HOH682 |
| site_id | AD7 |
| Number of Residues | 2 |
| Details | binding site for residue CL B 310 |
| Chain | Residue |
| B | LYS40 |
| B | PHE104 |
| site_id | AD8 |
| Number of Residues | 1 |
| Details | binding site for residue CL B 311 |
| Chain | Residue |
| B | HOH666 |
| site_id | AD9 |
| Number of Residues | 6 |
| Details | binding site for residue CL B 312 |
| Chain | Residue |
| B | SER151 |
| B | THR152 |
| B | PHE167 |
| B | SER168 |
| B | PHE169 |
| B | HOH493 |
| site_id | AE1 |
| Number of Residues | 3 |
| Details | binding site for residue IOD B 313 |
| Chain | Residue |
| A | ARG222 |
| B | LYS71 |
| B | HOH564 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 146 |
| Details | Domain: {"description":"5'-3' exonuclease","evidences":[{"source":"HAMAP-Rule","id":"MF_04140","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 68 |
| Details | Region: {"description":"Helical arch","evidences":[{"source":"HAMAP-Rule","id":"MF_04140","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"27273516","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8657312","evidenceCode":"ECO:0000305"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 72 |
| Details | Region: {"description":"DNA-binding; H3TH","evidences":[{"source":"HAMAP-Rule","id":"MF_04140","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"27273516","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_04140","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"10364212","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 10 |
| Details | Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_04140","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"27273516","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 2 |
| Details | Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_04140","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"15077103","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"27273516","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8657312","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
Catalytic Information from CSA
| site_id | MCSA1 |
| Number of Residues | 10 |
| Details | M-CSA 549 |
| Chain | Residue | Details |
| A | ASP26 | metal ligand |
| A | ASP204 | metal ligand |
| A | ASP68 | metal ligand |
| A | LYS83 | electrostatic stabiliser, proton shuttle (general acid/base) |
| A | ARG86 | electrostatic stabiliser |
| A | GLU128 | metal ligand |
| A | ASP131 | metal ligand |
| A | LYS153 | metal ligand |
| A | ASP155 | metal ligand |
| A | ASP201 | metal ligand |
| site_id | MCSA2 |
| Number of Residues | 10 |
| Details | M-CSA 549 |
| Chain | Residue | Details |
| B | ASP26 | metal ligand |
| B | ASP204 | metal ligand |
| B | ASP68 | metal ligand |
| B | LYS83 | electrostatic stabiliser, proton shuttle (general acid/base) |
| B | ARG86 | electrostatic stabiliser |
| B | GLU128 | metal ligand |
| B | ASP131 | metal ligand |
| B | LYS153 | metal ligand |
| B | ASP155 | metal ligand |
| B | ASP201 | metal ligand |
