MolNFT v1 · #184320 · protein + DNA
Crystal structure of kod DNA polymerase in a binary complex with hypoxanthine containing template
7OM3 · DNA POLYMERASE,DNA POLYMERASE,DNA polymerase: “Crystal structure of kod DNA polymerase in a binary complex with hypoxanthine containing template”. X-ray diffraction, 1 ligand (BR), 9 pockets (best druggability 0.79). MolNFT v1…
- PDB
- 7OM3
- Type
- protein + DNA
- Length
- 792 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA POLYMERASE,DNA POLYMERASE,DNA polymerase; 21NT template; Primer
- EC
- 2.7.7.7
- UniProt
- P77933
- Ligands
- BR
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 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) | protein | 759 | 42% helix, 23% strand | P77933 |
| T | 21NT template | dna | 21 | — | — |
| P | Primer | dna | 12 | — | — |
Ligands and binding sites
- BR · Bromide ion · ion · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, T
- PEG · Di(hydroxyethyl)ether · additive · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1169 | 0.79 | 0.80 | 70 | GOL |
| 2 | 117 | 0.75 | 0.96 | 33 | empty |
| 3 | 1049 | 0.73 | 0.76 | 86 | empty |
| 4 | 82 | 0.71 | 0.95 | 22 | empty |
| 5 | 190 | 0.58 | 0.80 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–T · 2075 Ų buried · 46 hydrogen bonds · protein-nucleic
- A–P · 757 Ų buried · 23 hydrogen bonds · protein-nucleic
- T–P · 549 Ų buried · 45 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 7OM3 · Crystal structure of KOD DNA Polymerase in a binary complex with Hypoxanthine 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 7OM3 · PDBe 7OM3 · UniProt P77933
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