Research workbench
Crystal structure of kod DNA polymerase in a ternary complex with a P/T duplex containing an extended 5' single stranded template overhang
Analyse Crystal structure of kod DNA polymerase in a ternary complex with a P/T duplex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OMB
- Type
- protein + DNA
- Length
- 789 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, MN, MG
- Pockets
- 7 · best druggability 0.79
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 | 756 | 43% helix, 23% strand | P77933 |
| T | Template | dna | 21 | — | — |
| P | Primer | dna | 12 | — | — |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · chains A, T, P
- MN · Manganese (II) ion · metal · 4 copies · chains A, P
- MG · Magnesium ion · metal · 2 copies · chains A, P
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, T, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 672 | 0.79 | 0.84 | 78 | DTP, MG, MN |
| 2 | 186 | 0.76 | 0.92 | 33 | MN |
| 3 | 396 | 0.71 | 0.82 | 43 | EDO |
| 4 | 91 | 0.61 | 0.89 | 25 | MG |
| 5 | 149 | 0.56 | 0.82 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1713 Ų buried · 38 hydrogen bonds · protein-nucleic
- A–P · 711 Ų buried · 22 hydrogen bonds · protein-nucleic
- T–P · 552 Ų buried · 48 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 disulfide, 1 modified (disulfide, nucleotide modification).
Compared structures
- 7OMB · Crystal structure of KOD DNA Polymerase in a ternary complex with a p/t duplex containing… · the same entry in another collection · chain A against A, 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 7OMB · PDBe 7OMB · UniProt P77933
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