Research workbench
Structure of 9N-I DNA polymerase incorporation with 3'-al in the active site
Analyse Structure of 9N-I DNA polymerase incorporation with 3'-al in the active site in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ISH
- Type
- protein + DNA
- Length
- 786 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*(DAL))-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q56366
- Ligands
- PPV, B9X, CA
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase (EC 2.7.7.7) | protein | 757 | 40% helix, 21% strand | Q56366 |
| C | DNA (5'- D(P*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*CP*(DAL))-3') | dna | 13 | — | — |
| D | DNA (5'- D(*AP*CP*TP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*C)-3') | dna | 16 | — | — |
Ligands and binding sites
- PPV · Pyrophosphate · ligand · chains A
- B9X · [(2R,3S,5R)-5-(6-aminopurin-9-yl)-2-(phosphonooxymethyl)oxolan-3-yl] 3-(2-ethoxyethoxy) propanoate · ligand · chains A, C, D
- CA · Calcium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 234 | 0.73 | 0.89 | 34 | empty |
| 2 | 196 | 0.72 | 0.89 | 40 | empty |
| 3 | 626 | 0.70 | 0.78 | 51 | empty |
| 4 | 119 | 0.62 | 0.86 | 26 | empty |
| 5 | 231 | 0.61 | 0.81 | 44 | empty |
Interfaces
3 interfaces between chains.
- A–D · 998 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–C · 620 Ų buried · 18 hydrogen bonds · protein-nucleic
- C–D · 589 Ų buried · 48 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 6ISH · Structure of 9N-I DNA polymerase incorporation with 3'-AL in the active site · the same entry in another collection · chain D against D, 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 6ISH · PDBe 6ISH · UniProt Q56366
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