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Ternary complex of 9N DNA polymerase in the replicative state with two metal ions in the active site
Analyse Ternary complex of 9N DNA polymerase in the replicative state with two metal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OMV
- Type
- protein + DNA
- Length
- 785 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase; DNA template; DNA primer
- EC
- 2.7.7.7
- UniProt
- Q56366
- Ligands
- DTP, MG, MN
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase (EC 2.7.7.7) | protein | 758 | 43% helix, 23% strand | Q56366 |
| T | DNA template | dna | 15 | — | — |
| P | DNA primer | dna | 12 | — | — |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · chains A, T, P
- MG · Magnesium ion · metal · 2 copies · chains A, P, T
- MN · Manganese (II) ion · metal · chains A
- PGE · Triethylene glycol · additive · 2 copies · chains A
- GOL · Glycerol · additive · chains A, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 913 | 0.82 | 0.84 | 98 | MN, PGE, DTP |
| 2 | 208 | 0.74 | 0.90 | 32 | empty |
| 3 | 424 | 0.63 | 0.77 | 53 | empty |
| 4 | 87 | 0.33 | 0.73 | 18 | empty |
| 5 | 92 | 0.32 | 0.73 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1220 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–P · 760 Ų buried · 23 hydrogen bonds · protein-nucleic
- T–P · 550 Ų buried · 47 hydrogen bonds · nucleic-nucleic
Compared structures
- 5OMV · Ternary complex of 9N DNA polymerase in the replicative state with two metal ions in the… · the same entry in another collection · chain A against A, TM-score 1.00
- Q56366 · AlphaFold monomer V2.0 prediction for DNA polymerase (Q56366) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q56366
- Elsewhere: RCSB PDB 5OMV · PDBe 5OMV · UniProt Q56366
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