MolNFT v1 · #40299 · protein + DNA
Mechanism of template-independent nucleotide incorporation catalyzed by a template-dependent DNA polymerase
2IMW · 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3': “Mechanism of template-independent nucleotide incorporation catalyzed by a template-dependent DNA polymerase”. X-ray diffraction, 2 ligands (DDS, CA), 2 pockets (best druggability…
- PDB
- 2IMW
- Type
- protein + DNA
- Length
- 376 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3'…
- EC
- 2.7.7.7
- UniProt
- Q97W02
- Ligands
- DDS, CA
- Pockets
- 2 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| S | 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3' | dna | 13 | — | — |
| T | 5'-D(*TP*AP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3' | dna | 15 | — | — |
| P | DNA polymerase IV (EC 2.7.7.7) | protein | 348 | 43% helix, 24% strand | Q97W02 |
Ligands and binding sites
- DDS · 2',3'-dideoxyadenosine triphosphate · ligand · chains S, T, P
- CA · Calcium ion · metal · 2 copies · chains P, T
- EDO · 1,2-ethanediol · additive · 6 copies · chains S, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1013 | 0.81 | 0.83 | 78 | CA, DDS, EDO |
| 2 | 324 | 0.75 | 0.87 | 32 | EDO |
Interfaces
3 interfaces between chains.
- T–P · 566 Ų buried · 18 hydrogen bonds · protein-nucleic
- S–T · 565 Ų buried · 58 hydrogen bonds · nucleic-nucleic
- S–P · 538 Ų buried · 15 hydrogen bonds · protein-nucleic
Compared structures
- 2IMW · Mechanism of Template-Independent Nucleotide Incorporation Catalyzed by a… · the same entry in another collection · chain S against S, TM-score 1.00
- Q97W02 · AlphaFold monomer V2.0 prediction for DNA polymerase IV (Q97W02) · a predicted model of the same protein · chain P against A, TM-score 0.96
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 Q97W02
- Elsewhere: RCSB PDB 2IMW · PDBe 2IMW · UniProt Q97W02
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.