Research workbench
Crystal structure of the large fragment of DNA polymerase I from thermus aquaticus in an open binary complex with D5SICS as templating nucleotide
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
- 4CCH
- Type
- protein + DNA
- Length
- 553 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 0.71
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 | 528 | 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*CP*LHOP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP* C)-3' | dna | 13 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains B, C
- FMT · Formic acid · additive · 4 copies · chains A, C
- GOL · Glycerol · additive · chains B, C
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 | 191 | 0.71 | 0.89 | 23 | empty |
| 2 | 273 | 0.60 | 0.79 | 31 | empty |
| 3 | 269 | 0.58 | 0.78 | 27 | empty |
| 4 | 214 | 0.52 | 0.76 | 21 | empty |
| 5 | 253 | 0.47 | 0.73 | 30 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1046 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–B · 814 Ų buried · 23 hydrogen bonds · protein-nucleic
- B–C · 553 Ų buried · 49 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 4CCH · 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 4CCH · PDBe 4CCH · UniProt P19821
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