Research workbench
T7 DNA polymerase ternary complex with 8 oxo guanosine and damp at the elongation site
Analyse T7 DNA polymerase ternary complex with 8 oxo guanosine and damp at the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TK8
- Type
- protein + DNA
- Length
- 834 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'- D(*CP*GP*AP*AP*AP*AP*CP*GP*AP*CP*GP*GP*CP*CP*AP*GP*TP*GP*CP *CP*AP*(2DA))-3'…
- EC
- 2.7.7.7
- UniProt
- P00581, P0AA25
- Ligands
- D3T, MG, SO4
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | 5'- D(*CP*GP*AP*AP*AP*AP*CP*GP*AP*CP*GP*GP*CP*CP*AP*GP*TP*GP*CP *CP*AP*(2DA))-3' | dna | 17 | — | — |
| T | 5'-D(*CP*CP*CP*AP*(8OG) P*TP*GP*GP*CP*AP*CP*TP*GP*GP*CP*CP*GP*TP*CP*GP*TP*TP*TP*TP* CP*G)-3' | dna | 20 | — | — |
| A | DNA polymerase (EC 2.7.7.7) | protein | 692 | 47% helix, 14% strand | P00581 |
| B | Thioredoxin 1 | protein | 105 | 38% helix, 28% strand | P0AA25 |
Ligands and binding sites
- D3T · 2',3'-dideoxy-thymidine-5'-triphosphate · ligand · chains P, T, A
- MG · Magnesium ion · metal · 4 copies · chains T, A, P
- SO4 · Sulfate ion · ion · 2 copies · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
- 1PE · Pentaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1026 | 0.78 | 0.81 | 88 | MG, D3T |
| 2 | 695 | 0.75 | 0.80 | 68 | MG, SO4, 1PE |
| 3 | 637 | 0.72 | 0.80 | 54 | MG |
| 4 | 78 | 0.38 | 0.77 | 15 | empty |
| 5 | 105 | 0.38 | 0.75 | 16 | empty |
Interfaces
4 interfaces between chains.
- T–A · 1191 Ų buried · 30 hydrogen bonds · protein-nucleic
- A–B · 1151 Ų buried · 9 hydrogen bonds · protein-protein
- P–T · 809 Ų buried · 60 hydrogen bonds · nucleic-nucleic
- P–A · 790 Ų buried · 11 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 1TK8 · T7 DNA polymerase ternary complex with 8 oxo guanosine and dAMP at the elongation site · the same entry in another collection · chain P against P, TM-score 1.00
- P0AA25 · AlphaFold monomer V2.0 prediction for thioredoxin 1 (P0AA25) · a predicted model of the same protein · chain B against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P00581
- Every structure of UniProt P0AA25
- Elsewhere: RCSB PDB 1TK8 · PDBe 1TK8 · UniProt P00581 · UniProt P0AA25
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.