MolNFT v1 · #141005 · protein + DNA
Large fragment of DNA polymerase I from thermus aquaticus in a closed ternary complex with the natural base pair 5FC:DGTP
5YTD: “Large fragment of DNA polymerase I from thermus aquaticus in a closed ternary complex with the natural base…”. X-ray diffraction, 2 ligands (DGT, MG). MolNFT v1 #141005 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5YTD
- Type
- protein + DNA
- Length
- 567 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- UniProt
- P19821
- Ligands
- DGT, MG
Structure
x-ray diffraction · 3 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | — | protein | 539 | — | P19821 |
| B | — | dna | 12 | — | — |
| C | — | dna | 16 | — | — |
Ligands and binding sites
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · chains A, B, C
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Compared structures
- 5YTD · large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex… · the same entry in another collection · chain A against A, TM-score 1.00
- P19821 · AlphaFold monomer V2.0 prediction for DNA polymerase I, thermostable (P19821) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P19821
- Elsewhere: RCSB PDB 5YTD · PDBe 5YTD · UniProt P19821
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