MolNFT v1 · #129522 · protein + DNA
Ternary complex of 9N DNA polymerase in the replicative state with two metal ions in the active site
5OMV: “Ternary complex of 9N DNA polymerase in the replicative state with two metal ions in the active site”. X-ray diffraction, 3 ligands (DTP, MG, MN), 6 pockets (best druggability 0.82). MolNFT v1 #129522 on GenesisL1: 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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