Research workbench
Structure of T7 DNA polymerase bound to a PRIMER/TEMPLATE DNA and a peptide that mimics the C-terminal tail of the primase-helicase
Analyse Structure of T7 DNA polymerase bound to a PRIMER/TEMPLATE DNA and a peptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P7E
- Type
- protein + DNA
- Length
- 3,317 residues
- Chains
- 19
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed DNA polymerase; Trxa; DNA (5'- D(P*GP*GP*CP*AP*GP*GP*TP*GP*GP*TP*CP*TP*TP*GP*…
- EC
- 2.7.7.7, 3.1.11.-
- UniProt
- P00581, Q14F07
- Ligands
- TTP, MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 11 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed DNA polymerase (EC 2.7.7.7, 3.1.11.-) | protein | 694 | 47% helix, 16% strand | P00581 |
| B | DNA-directed DNA polymerase (EC 2.7.7.7, 3.1.11.-) | protein | 697 | 47% helix, 15% strand | P00581 |
| C | DNA-directed DNA polymerase (EC 2.7.7.7, 3.1.11.-) | protein | 672 | 49% helix, 14% strand | P00581 |
| D | DNA-directed DNA polymerase (EC 2.7.7.7, 3.1.11.-) | protein | 644 | 51% helix, 13% strand | P00581 |
| E, F, G, H | Trxa | protein | 105 | 38% helix, 30% strand | Q14F07 |
| I, K, M, O | DNA (5'- D(P*GP*GP*CP*AP*GP*GP*TP*GP*GP*TP*CP*TP*TP*GP*CP*CP*GP*GP*TP*GP*A)- 3') | dna | 21 | — | — |
| J | DNA (25-mer) | dna | 25 | — | — |
| L, P | DNA (25-mer) | dna | 23 | — | — |
| N | DNA (25-mer) | dna | 24 | — | — |
| U, V | Asp-thr-asp-phe peptide | protein | 4 | 0% helix, 0% strand | — |
| W | Thr-asp-phe peptide | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · 8 copies · chains A, I, J, B, K, L, C, M, N, D, O, P
- MG · Magnesium ion · metal · 12 copies · chains A, I, B, K, C, M, D, O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1062 | 0.81 | 0.83 | 96 | TTP |
| 2 | 1099 | 0.80 | 0.82 | 91 | MG, TTP |
| 3 | 365 | 0.76 | 0.87 | 40 | empty |
| 4 | 920 | 0.75 | 0.79 | 78 | empty |
| 5 | 578 | 0.74 | 0.82 | 56 | MG, TTP |
Interfaces
28 interfaces between chains.
- A–J · 1389 Ų buried · 21 hydrogen bonds · protein-nucleic
- B–L · 1343 Ų buried · 23 hydrogen bonds · protein-nucleic
- C–N · 1286 Ų buried · 26 hydrogen bonds · protein-nucleic
- A–E · 1133 Ų buried · 14 hydrogen bonds · protein-protein
- B–F · 1130 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 6P7E · Structure of T7 DNA Polymerase Bound to a Primer/Template DNA and a Peptide that Mimics… · the same entry in another collection · chain A against A, 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 6P7E · PDBe 6P7E · UniProt P00581 · UniProt Q14F07
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