Research workbench
Tna polymerase, closed ternary complex
Analyse Tna polymerase, closed ternary complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VU8
- Type
- protein + DNA
- Length
- 783 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase; DNA template; DNA/TNA hybrid primer
- EC
- 2.7.7.7
- UniProt
- D0VWU9
- Ligands
- 9O7, MG
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase (EC 2.7.7.7) | protein | 757 | 37% helix, 21% strand | D0VWU9 |
| T | DNA template | dna | 14 | — | — |
| P | DNA/TNA hybrid primer | dna | 12 | — | — |
Ligands and binding sites
- 9O7 · [(3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-oxolan-3-yl] [oxidanyl(phosphonooxy)phosphoryl] hydrogen phosphate · ligand · chains A, T, P
- MG · Magnesium ion · metal · 3 copies · chains A, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 276 | 0.78 | 0.91 | 43 | empty |
| 2 | 950 | 0.77 | 0.80 | 91 | 9O7, MG |
| 3 | 525 | 0.65 | 0.76 | 54 | empty |
| 4 | 192 | 0.56 | 0.80 | 35 | empty |
| 5 | 128 | 0.39 | 0.74 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1077 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–P · 721 Ų buried · 15 hydrogen bonds · protein-nucleic
- T–P · 506 Ų buried · 47 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 disulfide, 1 modified (disulfide, nucleotide modification).
Compared structures
- 5VU8 · TNA polymerase, closed ternary complex · 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 D0VWU9
- Elsewhere: RCSB PDB 5VU8 · PDBe 5VU8 · UniProt D0VWU9
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