5HMM
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 | 3 |
| Details | binding site for residue EDO A 301 |
| Chain | Residue |
| A | ARG216 |
| A | LYS241 |
| A | TYR242 |
| site_id | AC2 |
| Number of Residues | 7 |
| Details | binding site for residue MG A 302 |
| Chain | Residue |
| A | HOH642 |
| A | ASP130 |
| A | MG303 |
| A | HOH425 |
| A | HOH438 |
| A | HOH440 |
| A | HOH524 |
| site_id | AC3 |
| Number of Residues | 5 |
| Details | binding site for residue MG A 303 |
| Chain | Residue |
| A | ASP130 |
| A | ASP153 |
| A | ASP155 |
| A | MG302 |
| A | HOH524 |
| site_id | AC4 |
| Number of Residues | 6 |
| Details | binding site for residue MG A 304 |
| Chain | Residue |
| A | ASP155 |
| A | ASP201 |
| A | HOH401 |
| A | HOH418 |
| A | HOH532 |
| A | HOH556 |
| site_id | AC5 |
| Number of Residues | 2 |
| Details | binding site for residue CL A 305 |
| Chain | Residue |
| B | GLY211 |
| B | HOH459 |
| site_id | AC6 |
| Number of Residues | 2 |
| Details | binding site for residue CL A 306 |
| Chain | Residue |
| A | ARG178 |
| A | HOH640 |
| site_id | AC7 |
| Number of Residues | 6 |
| Details | binding site for residue MG B 301 |
| Chain | Residue |
| B | ASP130 |
| B | HOH412 |
| B | HOH429 |
| B | HOH438 |
| B | HOH462 |
| B | HOH676 |
| site_id | AC8 |
| Number of Residues | 6 |
| Details | binding site for residue MG B 302 |
| Chain | Residue |
| B | ASP201 |
| B | HOH449 |
| B | HOH452 |
| B | HOH506 |
| B | HOH604 |
| B | HOH682 |
| site_id | AC9 |
| Number of Residues | 6 |
| Details | binding site for residue MG B 303 |
| Chain | Residue |
| B | ASP87 |
| B | HOH401 |
| B | HOH418 |
| B | HOH443 |
| B | HOH594 |
| B | HOH600 |
| site_id | AD1 |
| Number of Residues | 4 |
| Details | binding site for residue CL B 304 |
| Chain | Residue |
| A | HOH624 |
| B | GLY213 |
| B | ARG216 |
| B | HOH686 |
| site_id | AD2 |
| Number of Residues | 2 |
| Details | binding site for residue CL B 305 |
| Chain | Residue |
| B | ALA44 |
| B | SER45 |
| site_id | AD3 |
| Number of Residues | 2 |
| Details | binding site for residue CL B 306 |
| Chain | Residue |
| A | ARG222 |
| B | HOH654 |
| site_id | AD4 |
| Number of Residues | 3 |
| Details | binding site for residue CL B 307 |
| Chain | Residue |
| B | LYS239 |
| B | HOH601 |
| B | HOH633 |
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 | ASP153 | |
| B | ASP153 |
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 | ASP153 | 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 | ASP153 | metal ligand |
| B | ASP155 | metal ligand |
| B | ASP201 | metal ligand |
