Research workbench
Snapshot of the large fragment of DNA polymerase I from thermus aquaticus processing C5 modified thymidies
Analyse Snapshot of the large fragment of DNA polymerase I from thermus aquaticus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OJU
- Type
- protein + DNA
- Length
- 565 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase I, thermostable; DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3')…
- EC
- 2.7.7.7
- UniProt
- P19821
- Ligands
- SSJ, MG
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 53% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase I, thermostable (EC 2.7.7.7) | protein | 539 | 53% helix, 13% strand | P19821 |
| B | DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3') | dna | 12 | — | — |
| C | DNA (5'-D(*AP*AP*AP*AP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)- 3') | dna | 14 | — | — |
Ligands and binding sites
- SSJ · 2'-deoxy-5-[(1-hydroxy-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)ethynyl]uridine 5'-(tetrahydrogen triphosphate) · ligand · chains A, B, C
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PGE · Triethylene glycol · additive · 11 copies · chains A, C
- GOL · Glycerol · additive · 6 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1054 | 0.74 | 0.77 | 69 | SSJ, MG |
| 2 | 233 | 0.71 | 0.87 | 26 | GOL |
| 3 | 278 | 0.61 | 0.80 | 33 | GOL |
| 4 | 182 | 0.45 | 0.74 | 21 | PGE |
| 5 | 74 | 0.42 | 0.80 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1157 Ų buried · 27 hydrogen bonds · protein-nucleic
- A–B · 792 Ų buried · 27 hydrogen bonds · protein-nucleic
- B–C · 563 Ų buried · 54 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3OJU · Snapshot of the large fragment of DNA polymerase I from Thermus Aquaticus processing c5… · 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 0.97
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 3OJU · PDBe 3OJU · UniProt P19821
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