Research workbench
Kod DNA pol in a closed ternary complex with 7-deaza-7-(2-(2- hydroxyethoxy)-N-(prop-2-yn-1-YL)ACETAMIDE)-2-datp
Analyse Kod DNA pol in a closed ternary complex with 7-deaza-7-(2-(2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Q4T
- Type
- protein + DNA
- Length
- 785 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA POLYMERASE,DNA POLYMERASE,DNA polymerase; DNA (5'…
- EC
- 2.7.7.7, 3.1.-.-
- UniProt
- P77933
- Ligands
- HHZ, MG, MN, NO3, SO4
- Pockets
- 8 · best druggability 0.81
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, 3.1.-.-) | protein | 757 | 42% helix, 23% strand | P77933 |
| T | DNA (5'- D(P*AP*AP*CP*TP*GP*TP*GP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3') | dna | 16 | — | — |
| P | DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*CP*AP*C)-3') | dna | 12 | — | — |
Ligands and binding sites
- HHZ · [[(2~{R},3~{S},5~{R})-5-[4-azanyl-5-[3-[2-(2-hydroxyethyloxy)ethanoylamino]prop-1-ynyl]pyrrolo[2,3-d]pyrimidin-7-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate · ligand · chains A, T, P
- MG · Magnesium ion · metal · 2 copies · chains A, P, T
- MN · Manganese (II) ion · metal · chains A
- NO3 · Nitrate ion · ion · 2 copies · chains A
- SO4 · Sulfate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 932 | 0.81 | 0.83 | 83 | MN, MG, EDO, HHZ |
| 2 | 193 | 0.77 | 0.93 | 35 | empty |
| 3 | 264 | 0.59 | 0.79 | 37 | EDO |
| 4 | 213 | 0.52 | 0.77 | 37 | EDO |
| 5 | 100 | 0.47 | 0.80 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1379 Ų buried · 31 hydrogen bonds · protein-nucleic
- A–P · 725 Ų buried · 20 hydrogen bonds · protein-nucleic
- T–P · 551 Ų buried · 50 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6Q4T · KOD DNA pol in a closed ternary complex with 7-deaza-7-(2-(2-hydroxyethoxy)-N-(prop-2-yn-1… · 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 6Q4T · PDBe 6Q4T · UniProt P77933
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