Research workbench
Structure of replicative DNA polymerase provides insigts into the mechanisms for processivity, frameshifting and editing
Analyse Structure of replicative DNA polymerase provides insigts into the mechanisms… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AJQ
- Type
- protein + DNA
- Length
- 1,690 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA primer; DNA template; T7 DNA polymerase; Thioredoxin 1
- EC
- 2.7.7.7
- UniProt
- P00581, P0AA25
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 7 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | DNA primer | dna | 19 | — | — |
| T | DNA template | dna | 22 | — | — |
| X | DNA primer | dna | 21 | — | — |
| Z | DNA template | dna | 25 | — | — |
| A | T7 DNA polymerase (EC 2.7.7.7) | protein | 704 | 48% helix, 15% strand | P00581 |
| B, I | Thioredoxin 1 | protein | 105 | 32% helix, 28% strand | P0AA25 |
| F | T7 DNA polymerase (EC 2.7.7.7) | protein | 689 | 47% helix, 15% strand | P00581 |
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1069 | 0.75 | 0.78 | 96 | empty |
| 2 | 1078 | 0.74 | 0.77 | 76 | empty |
| 3 | 844 | 0.72 | 0.77 | 73 | empty |
| 4 | 813 | 0.71 | 0.77 | 65 | empty |
| 5 | 396 | 0.61 | 0.77 | 43 | empty |
Interfaces
10 interfaces between chains.
- Z–F · 1408 Ų buried · 24 hydrogen bonds · protein-nucleic
- T–A · 1331 Ų buried · 24 hydrogen bonds · protein-nucleic
- F–I · 1199 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1106 Ų buried · 13 hydrogen bonds · protein-protein
- X–Z · 977 Ų buried · 78 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 2AJQ · Structure of replicative DNA polymerase provides insigts into the mechanisms for… · the same entry in another collection · chain I against I, TM-score 1.00
- P0AA25 · AlphaFold monomer V2.0 prediction for thioredoxin 1 (P0AA25) · a predicted model of the same protein · chain B 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 P00581
- Every structure of UniProt P0AA25
- Elsewhere: RCSB PDB 2AJQ · PDBe 2AJQ · UniProt P00581 · UniProt P0AA25
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