MolNFT v1 · #161138 · protein + DNA
Klentaq DNA pol in a closed ternary complex with 7-deaza-7-(2-(2- hydroxyethoxy)-N-(prop-2-yn-1-YL)ACETAMIDE)-2-datp
6Q4U · DNA polymerase I, thermostable: “Klentaq DNA pol in a closed ternary complex with 7-deaza-7-(2-(2…”. X-ray diffraction, 3 ligands (HHZ, MG, MN), 7 pockets (best druggability 0.79). MolNFT v1 #161138 on GenesisL1: 3D structure…
- PDB
- 6Q4U
- Type
- protein + DNA
- Length
- 567 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase I, thermostable; DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*CP*AP*(DOC))-3')…
- EC
- 2.7.7.7
- UniProt
- P19821
- Ligands
- HHZ, MG, MN
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase I, thermostable (EC 2.7.7.7) | protein | 539 | 54% helix, 13% strand | P19821 |
| B | DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*CP*AP*(DOC))-3') | dna | 12 | — | — |
| C | DNA (5'-D(*AP*AP*CP*TP*GP*TP*GP*GP*CP*CP*GP*TP*GP*GP*TP*C)- 3') | dna | 16 | — | — |
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, B, C
- MG · Magnesium ion · metal · 2 copies · chains A, B, C
- MN · Manganese (II) ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, C, B
- GOL · Glycerol · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 904 | 0.79 | 0.82 | 67 | MG, MN, HHZ |
| 2 | 232 | 0.70 | 0.87 | 25 | empty |
| 3 | 297 | 0.61 | 0.79 | 34 | empty |
| 4 | 129 | 0.54 | 0.81 | 19 | empty |
| 5 | 60 | 0.43 | 0.82 | 18 | EDO |
Interfaces
3 interfaces between chains.
- A–C · 1384 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–B · 813 Ų buried · 28 hydrogen bonds · protein-nucleic
- B–C · 563 Ų buried · 49 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
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 P19821
- Elsewhere: RCSB PDB 6Q4U · PDBe 6Q4U · UniProt P19821
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