Research workbench
DNA polymerase (E.C.2.7.7.7)/DNA complex
Analyse DNA polymerase (E.C.2.7.7.7)/DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NOY
- Type
- protein + DNA
- Length
- 721 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*TP*TP*T)-3'); Protein (DNA polymerase (E.C.2.7.7.7))
- UniProt
- P04415
- Ligands
- ZN, MN
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| S | DNA (5'-D(*TP*TP*T)-3') | dna | 3 | — | — |
| A | Protein (DNA polymerase (E.C.2.7.7.7)) | protein | 372 | 44% helix, 19% strand | P04415 |
| B | Protein (DNA polymerase (E.C.2.7.7.7)) | protein | 346 | 38% helix, 19% strand | P04415 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 644 | 0.70 | 0.78 | 61 | empty |
| 2 | 234 | 0.64 | 0.83 | 26 | empty |
| 3 | 332 | 0.63 | 0.79 | 39 | empty |
| 4 | 276 | 0.60 | 0.79 | 37 | empty |
| 5 | 290 | 0.54 | 0.75 | 29 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1543 Ų buried · 10 hydrogen bonds · protein-protein
- S–B · 448 Ų buried · 8 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1NOY · DNA polymerase (E.C.2.7.7.7)/DNA complex · the same entry in another collection · chain S against S, TM-score 1.00
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 P04415
- Elsewhere: RCSB PDB 1NOY · PDBe 1NOY · UniProt P04415
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