MolNFT v1 · #157712 · protein + DNA
Structure of bacteriophage T7 leading-strand DNA polymerase (D5A/E7A) /trx in complex with a DNA fork and incoming dttp (from multiple lead complexes)
6N7W · DNA-directed DNA polymerase: “Structure of bacteriophage T7 leading-strand DNA polymerase (D5A/E7A) /trx in complex with a DNA fork and…”. Electron microscopy, 2 ligands (TTP, MG), 11 pockets (best druggability 0.77). MolNFT v1…
- PDB
- 6N7W
- Type
- protein + DNA
- Length
- 878 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed DNA polymerase; Trxa; DNA (25-mer); DNA (77-mer)
- EC
- 2.7.7.7, 3.1.11.-
- UniProt
- P00581, Q14F07
- Ligands
- TTP, MG
- Pockets
- 11 · best druggability 0.77
Structure
electron microscopy · 4 distinct chains · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | DNA-directed DNA polymerase (EC 2.7.7.7, 3.1.11.-) | protein | 702 | 46% helix, 12% strand | P00581 |
| I | Trxa | protein | 106 | 33% helix, 27% strand | Q14F07 |
| P | DNA (25-mer) | dna | 25 | — | — |
| T | DNA (77-mer) | dna | 45 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 551 | 0.77 | 0.84 | 65 | empty |
| 2 | 532 | 0.75 | 0.83 | 51 | MG, TTP |
| 3 | 934 | 0.73 | 0.77 | 101 | empty |
| 4 | 50 | 0.66 | 0.96 | 14 | empty |
| 5 | 447 | 0.63 | 0.77 | 46 | empty |
Interfaces
5 interfaces between chains.
- H–T · 1413 Ų buried · 19 hydrogen bonds · protein-nucleic
- P–T · 1121 Ų buried · 88 hydrogen bonds · nucleic-nucleic
- H–I · 1058 Ų buried · 9 hydrogen bonds · protein-protein
- H–P · 870 Ų buried · 16 hydrogen bonds · protein-nucleic
- I–P · 23 Ų buried · 0 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6N7W · Structure of bacteriophage T7 leading-strand DNA polymerase (D5A/E7A)/Trx in complex with… · the same entry in another collection · chain H against H, 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 P00581
- Every structure of UniProt Q14F07
- Elsewhere: RCSB PDB 6N7W · PDBe 6N7W · UniProt P00581 · UniProt Q14F07
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