MolNFT v1 · #79292 · protein + DNA
Crystal structure of the large fragment of DNA polymerase I from thermus aquaticus in an open binary complex with dnam as templating nucleobase
3SYZ · DNA polymerase I, thermostable: “Crystal structure of the large fragment of DNA polymerase I from thermus aquaticus in an open binary complex…”. X-ray diffraction, 1 ligand (MG), 8 pockets (best druggability 0.69). MolNFT v1 #79292…
- PDB
- 3SYZ
- Type
- protein + DNA
- Length
- 568 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase I, thermostable; (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3')…
- EC
- 2.7.7.7
- UniProt
- P19821
- Ligands
- MG
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase I, thermostable (EC 2.7.7.7) | protein | 540 | 52% helix, 13% strand | P19821 |
| B | (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3') | dna | 12 | — | — |
| C | (5'-D(*AP*AP*AP*(BMN)P*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)- 3') | dna | 16 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 10 copies · chains A, C, B
- FMT · Formic acid · additive · 6 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 198 | 0.69 | 0.87 | 27 | empty |
| 2 | 386 | 0.64 | 0.78 | 44 | MG |
| 3 | 605 | 0.63 | 0.74 | 53 | MG, GOL |
| 4 | 283 | 0.61 | 0.79 | 33 | empty |
| 5 | 92 | 0.44 | 0.79 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1317 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–B · 805 Ų buried · 26 hydrogen bonds · protein-nucleic
- B–C · 599 Ų buried · 52 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3SYZ · Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in an… · 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 0.98
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 P19821
- Elsewhere: RCSB PDB 3SYZ · PDBe 3SYZ · UniProt P19821
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