Research workbench
Closed, ternary structure of KOD DNA polymerase
Analyse Closed, ternary structure of KOD DNA polymerase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OMF
- Type
- protein + DNA
- Length
- 782 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.092
- Source
- Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1); SYNTHETIC…
- Molecule
- DNA polymerase,DNA polymerase,DNA polymerase; DNA…
- EC
- 2.7.7.7, 3.1.-.-
- UniProt
- P77933
- Ligands
- DTP, MN, MG
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · resolution 2.092 · 3 distinct chains · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase,DNA polymerase,DNA polymerase (EC 2.7.7.7, 3.1.-.-) | protein | 756 | 42% helix, 23% strand | P77933 |
| T | DNA (5'-D(P*CP*TP*GP*TP*GP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3') | dna | 14 | — | — |
| P | DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*CP*AP*C)-3') | dna | 12 | — | — |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · chains A, T, P
- MN · Manganese (II) ion · metal · 2 copies · chains A
- MG · Magnesium ion · metal · chains A, P
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, T
- GOL · Glycerol · additive · 3 copies · chains A, P, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 890 | 0.77 | 0.80 | 82 | MN, MG, GOL, DTP |
| 2 | 182 | 0.76 | 0.93 | 35 | EDO |
| 3 | 378 | 0.60 | 0.76 | 48 | empty |
| 4 | 60 | 0.43 | 0.82 | 16 | EDO |
| 5 | 68 | 0.36 | 0.77 | 16 | EDO |
Interfaces
3 interfaces between chains.
- A–T · 1084 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–P · 725 Ų buried · 22 hydrogen bonds · protein-nucleic
- T–P · 553 Ų buried · 54 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
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 5OMF · PDBe 5OMF · UniProt P77933
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.