Research workbench
Crystal structure of the large fragment of DNA polymerase I from thermus aquaticus in a partially closed complex with the artificial base pair D5SICS-dnamtp
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
- 4C8K
- Type
- protein + DNA
- Length
- 566 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*C*DOC)-3'…
- EC
- 2.7.7.7
- UniProt
- P19821
- Ligands
- BMR, MG
- Pockets
- 9 · best druggability 0.70
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 | 540 | 53% helix, 13% strand | P19821 |
| B | 5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*C*DOC)-3' | dna | 12 | — | — |
| C | 5'-D(*AP*AP*C*LHOP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3' | dna | 14 | — | — |
Ligands and binding sites
- BMR · ((2R,3S,5R)-3-hydroxy-5-(3-methoxynaphthalen-2-yl)methyl-tetrahydrogen-triphosphate · ligand · chains A, B, C
- MG · Magnesium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B, C
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 219 | 0.70 | 0.87 | 26 | empty |
| 2 | 850 | 0.69 | 0.76 | 55 | BMR, MG, TRS |
| 3 | 281 | 0.59 | 0.79 | 34 | empty |
| 4 | 102 | 0.59 | 0.86 | 18 | empty |
| 5 | 211 | 0.47 | 0.75 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1120 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–B · 788 Ų buried · 23 hydrogen bonds · protein-nucleic
- B–C · 563 Ų buried · 48 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 4C8K · Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in a… · 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 0.99
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 4C8K · PDBe 4C8K · UniProt P19821
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