MolNFT v1 · #87296 · protein + DNA + RNA
Klentaq mutant in complex with a RNA/DNA hybrid
4BWM · DNA polymerase I, thermostable: “Klentaq mutant in complex with a RNA/DNA hybrid”. X-ray diffraction, 3 ligands (DCT, MG, CL), 6 pockets (best druggability 0.83). MolNFT v1 #87296 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4BWM
- Type
- protein + DNA + RNA
- Length
- 562 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*DOCP)-3'…
- EC
- 2.7.7.7
- UniProt
- P19821
- Ligands
- DCT, MG, CL
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 55% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase I, thermostable (EC 2.7.7.7) | protein | 538 | 55% helix, 14% strand | P19821 |
| B | 5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*DOCP)-3' | dna | 10 | — | — |
| G | 5'-R(*AP*AP*AP*GP*GP*GP*CP*GP*CP*CP*GP*UP*GP*GP*UP*C)-3' | rna | 14 | — | — |
Ligands and binding sites
- DCT · 2',3'-dideoxycytidine 5'-triphosphate · ligand · chains A, B, G
- MG · Magnesium ion · metal · 3 copies · chains A, B, G
- CL · Chloride ion · ion · 2 copies · chains A
- FMT · Formic acid · additive · 4 copies · chains A, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 950 | 0.83 | 0.85 | 87 | DCT, MG, FMT |
| 2 | 255 | 0.59 | 0.79 | 32 | empty |
| 3 | 232 | 0.52 | 0.76 | 24 | empty |
| 4 | 64 | 0.47 | 0.84 | 16 | FMT |
| 5 | 104 | 0.41 | 0.77 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–G · 1041 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–B · 566 Ų buried · 18 hydrogen bonds · protein-nucleic
- B–G · 511 Ų buried · 52 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
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 4BWM · PDBe 4BWM · UniProt P19821
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.