1RFI
Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, pentapeptide KLNYK, and tetranucleotide AGTC
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A, B (D, F) | 5'-D(*AP*GP*TP*C)-3' | polymer | 4 | 1190.8 | 2 | |||
| 2 | C, D (A, B) | Tyrosyl-DNA phosphodiesterase 1 | polymer | 485 | 54731.2 | 2 | UniProt (Q9NUW8) Pfam (PF06087) | Homo sapiens (human) | Tyr-DNA phosphodiesterase 1, TDP1 |
| 3 | E, F (C, E) | Topoisomerase I-Derived Peptide | polymer | 5 | 666.8 | 2 | |||
| 4 | G, I (A, B) | VANADATE ION | non-polymer | 114.9 | 2 | Chemie (VO4) | |||
| 5 | H (A) | SPERMINE | non-polymer | 202.3 | 1 | Chemie (SPM) | |||
| 6 | J, K, L, M, N (D, F, A, B, C) | water | water | 18.0 | 243 | Chemie (HOH) |
Sequence modifications
A, B: 149 - 608 (UniProt: Q9NUW8)
| PDB | External Database | Details |
|---|---|---|
| Met 124 | - | cloning artifact |
| Gly 125 | - | cloning artifact |
| Ser 126 | - | cloning artifact |
| Ser 127 | - | cloning artifact |
| His 128 | - | cloning artifact |
| His 129 | - | cloning artifact |
| His 130 | - | cloning artifact |
| His 131 | - | cloning artifact |
| His 132 | - | cloning artifact |
| His 133 | - | cloning artifact |
| Ser 134 | - | cloning artifact |
| Ser 135 | - | cloning artifact |
| Gly 136 | - | cloning artifact |
| Leu 137 | - | cloning artifact |
| Val 138 | - | cloning artifact |
| Pro 139 | - | cloning artifact |
| Arg 140 | - | cloning artifact |
| Gly 141 | - | cloning artifact |
| Ser 142 | - | cloning artifact |
| His 143 | - | cloning artifact |
| Met 144 | - | cloning artifact |
| Leu 145 | - | cloning artifact |
| Glu 146 | - | cloning artifact |
| Asp 147 | - | cloning artifact |
| Pro 148 | - | cloning artifact |
| Asn 322 | Asp 322 | engineered mutation |
| Thr 328 | Met 328 | engineered mutation |
| Leu 548 | Phe 548 | engineered mutation |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 6 |
| Total formula weight | 113177.7 | |
| Non-Polymers* | Number of molecules | 3 |
| Total formula weight | 432.2 | |
| All* | Total formula weight | 113609.9 |
