MolNFT v1 · #31106 · protein + DNA
Structure of replicative DNA polymerase provides insigts into the mechanisms for processivity, frameshifting and editing
2AJQ · DNA primer: “Structure of replicative DNA polymerase provides insigts into the mechanisms for processivity, frameshifting…”. X-ray diffraction, 20 pockets (best druggability 0.75). MolNFT v1 #31106 on GenesisL1: 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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