Research workbench
Crystal structure of kod DNA polymerase in a ternary complex with an uracil containing template
Analyse Crystal structure of kod DNA polymerase in a ternary complex with an uracil… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OMG
- Type
- protein + DNA
- Length
- 779 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase; Template; Primer
- EC
- 2.7.7.7
- UniProt
- P77933
- Ligands
- DTP, MG, CA, MN, CL
- Pockets
- 8 · best druggability 0.78
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 | 747 | 41% helix, 23% strand | P77933 |
| T | Template | dna | 20 | — | — |
| P | 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
- CA · Calcium ion · metal · 2 copies · chains A
- MN · Manganese (II) ion · metal · chains A
- CL · Chloride ion · ion · chains A, T
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 898 | 0.78 | 0.81 | 74 | DTP, MG |
| 2 | 191 | 0.74 | 0.91 | 37 | empty |
| 3 | 156 | 0.70 | 0.90 | 23 | empty |
| 4 | 365 | 0.60 | 0.77 | 37 | empty |
| 5 | 111 | 0.56 | 0.85 | 22 | CL |
Interfaces
3 interfaces between chains.
- A–T · 1858 Ų buried · 45 hydrogen bonds · protein-nucleic
- A–P · 734 Ų buried · 19 hydrogen bonds · protein-nucleic
- T–P · 550 Ų buried · 52 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 disulfide, 1 modified (disulfide, nucleotide modification).
Compared structures
- 7OMG · Crystal structure of KOD DNA Polymerase in a ternary complex with an Uracil containing… · the same entry in another collection · chain T against T, TM-score 1.00
- P77933 · AlphaFold monomer V2.0 prediction for DNA polymerase (P77933) · a predicted model of the same protein · chain A against A, TM-score 0.91
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 P77933
- Elsewhere: RCSB PDB 7OMG · PDBe 7OMG · UniProt P77933
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