MolNFT v2 · #129917 · protein + DNA
Closed, ternary structure of KOD DNA polymerase
5OMF: “Closed, ternary structure of KOD DNA polymerase”. X-ray diffraction at 2.092, 3 ligands (DTP, MN, MG). MolNFT v2 #129917 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- 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…
- UniProt
- P77933
- Ligands
- DTP, MN, MG
Structure
x-ray diffraction · resolution 2.092 · 3 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | — | protein | 756 | — | P77933 |
| T | — | dna | 14 | — | — |
| P | — | 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
- GOL · Glycerol · additive · 3 copies · chains A, P, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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
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