Research workbench
Crystal structure of the large fragment of DNA polymerase I from thermus aquaticus in an open binary complex with dg as templating nucleobase
Analyse Crystal structure of the large fragment of DNA polymerase I from thermus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SZ2
- Type
- protein + DNA
- Length
- 555 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*(DDG))-3')…
- EC
- 2.7.7.7
- UniProt
- P19821
- Ligands
- MG
- Pockets
- 8 · best druggability 0.70
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 | 530 | 52% helix, 13% strand | P19821 |
| B | (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DDG))-3') | dna | 12 | — | — |
| D | (5'-D(*AP*AP*AP*GP*CP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3') | dna | 13 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains B
- FMT · Formic acid · additive · 6 copies · chains A, D, B
- GOL · Glycerol · additive · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 208 | 0.70 | 0.88 | 27 | FMT |
| 2 | 286 | 0.60 | 0.79 | 33 | empty |
| 3 | 250 | 0.53 | 0.76 | 28 | empty |
| 4 | 410 | 0.53 | 0.72 | 27 | FMT |
| 5 | 199 | 0.52 | 0.77 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–D · 1003 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–B · 875 Ų buried · 28 hydrogen bonds · protein-nucleic
- B–D · 576 Ų buried · 55 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3SZ2 · 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 1.00
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 3SZ2 · PDBe 3SZ2 · UniProt P19821
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