1NOP
Crystal structure of human tyrosyl-DNA phosphodiesterase (Tdp1) in complex with vanadate, DNA and a human topoisomerase I-derived peptide
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*AP*GP*TP*T)-3' | polymer | 6 | 1848.3 | 2 | |||
| 2 | C, D (A, B) | tyrosyl-DNA phosphodiesterase 1 | polymer | 485 | 54731.2 | 2 | GenBank (20127586) Pfam (PF06087) UniProt (by SIFTS) (Q9NUW8) | Homo sapiens (human) | Tdp1 |
| 3 | E (C) | topoisomerase I-derived peptide | polymer | 8 | 1020.2 | 1 | |||
| 4 | F, G (A, B) | VANADATE ION | non-polymer | 114.9 | 2 | Chemie (VO4) | |||
| 5 | H, I, J, K (D, A, B, C) | water | water | 18.0 | 96 | Chemie (HOH) |
Sequence modifications
A, B: 149 - 608 (GenBank: 20127586)
| 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 | 5 |
| Total formula weight | 114179.1 | |
| Non-Polymers* | Number of molecules | 2 |
| Total formula weight | 229.9 | |
| All* | Total formula weight | 114409.0 |
