MolNFT v1 · #129517 · protein + DNA
Ternary complex of 9N DNA polymerase in the replicative state with three metal ions in the active site
5OMQ: “Ternary complex of 9N DNA polymerase in the replicative state with three metal ions in the active site”. X-ray diffraction, 3 ligands (DTP, MG, MN), 8 pockets (best druggability 0.81). MolNFT v1 #129517 on GenesisL1: 3D structure…
- PDB
- 5OMQ
- Type
- protein + DNA
- Length
- 784 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
- 8 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase (EC 2.7.7.7) | protein | 758 | 41% helix, 23% strand | Q56366 |
| T | DNA template | dna | 14 | — | — |
| 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
- MN · Manganese (II) ion · metal · chains A
- GOL · Glycerol · additive · chains A, P
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 948 | 0.81 | 0.83 | 85 | GOL, MG, MN, DTP |
| 2 | 137 | 0.77 | 0.95 | 28 | empty |
| 3 | 1064 | 0.73 | 0.77 | 61 | PGE |
| 4 | 115 | 0.53 | 0.82 | 27 | empty |
| 5 | 111 | 0.37 | 0.74 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1065 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–P · 752 Ų buried · 21 hydrogen bonds · protein-nucleic
- T–P · 548 Ų buried · 54 hydrogen bonds · nucleic-nucleic
Compared structures
- 5OMQ · Ternary complex of 9N DNA polymerase in the replicative state with three metal ions in… · 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 5OMQ · PDBe 5OMQ · UniProt Q56366
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