MolNFT v1 · #152766 · protein + DNA
Structure of 9N-I DNA polymerase incorporation with 3'-cl in the active site
6ISI: “Structure of 9N-I DNA polymerase incorporation with 3'-cl in the active site”. X-ray diffraction, 3 ligands (PPV, B0U, CA), 10 pockets (best druggability 0.76). MolNFT v1 #152766 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6ISI
- Type
- protein + DNA
- Length
- 785 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase; DNA (5'-D(P*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*CP*C)- 3'); DNA (5'…
- EC
- 2.7.7.7
- UniProt
- Q56366
- Ligands
- PPV, B0U, CA
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase (EC 2.7.7.7) | protein | 757 | 42% helix, 21% strand | Q56366 |
| C | DNA (5'-D(P*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*CP*C)- 3') | dna | 13 | — | — |
| D | DNA (5'- D(P*AP*CP*GP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3') | dna | 15 | — | — |
Ligands and binding sites
- PPV · Pyrophosphate · ligand · chains A
- B0U · 3-[2-[2-(2-azanylethoxy)ethoxy]ethoxy]propanoic acid · ligand · chains A, C, D
- CA · Calcium ion · metal · 4 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 286 | 0.76 | 0.89 | 38 | empty |
| 2 | 246 | 0.75 | 0.89 | 39 | empty |
| 3 | 765 | 0.74 | 0.79 | 70 | B0U, CA |
| 4 | 493 | 0.66 | 0.78 | 41 | empty |
| 5 | 306 | 0.63 | 0.80 | 44 | empty |
Interfaces
3 interfaces between chains.
- A–D · 983 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–C · 712 Ų buried · 22 hydrogen bonds · protein-nucleic
- C–D · 556 Ų buried · 47 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6ISI · Structure of 9N-I DNA polymerase incorporation with 3'-CL in the active site · the same entry in another collection · chain A against A, TM-score 1.00
- Q56366 · AlphaFold monomer V2.0 prediction for DNA polymerase (Q56366) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q56366
- Elsewhere: RCSB PDB 6ISI · PDBe 6ISI · UniProt Q56366
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.