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 | 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 | 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 | 0140640 | molecular_function | catalytic activity, acting on a nucleic acid |
A | 1990238 | molecular_function | double-stranded DNA endonuclease activity |
B | 0003677 | molecular_function | DNA binding |
B | 0003824 | molecular_function | catalytic 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 | 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 | 0140640 | molecular_function | catalytic activity, acting on a nucleic acid |
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 | 2 |
Details | BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_04140, ECO:0000269|PubMed:10364212 |
Chain | Residue | Details |
A | LYS83 | |
B | LYS83 |
site_id | SWS_FT_FI2 |
Number of Residues | 10 |
Details | BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_04140, ECO:0000269|PubMed:27273516 |
Chain | Residue | Details |
A | ASP130 | |
B | ILE212 | |
A | ASP155 | |
A | ASP201 | |
A | VAL209 | |
A | ILE212 | |
B | ASP130 | |
B | ASP155 | |
B | ASP201 | |
B | VAL209 |
site_id | SWS_FT_FI3 |
Number of Residues | 2 |
Details | BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_04140, ECO:0000269|PubMed:15077103, ECO:0000269|PubMed:27273516, ECO:0000269|PubMed:8657312 |
Chain | Residue | Details |
A | LYS153 | |
B | LYS153 |
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 |