MolNFT v1 · #78987 · protein + DNA
DNA POLYMERASE(L561A/S565G/Y567A) ternary complex with dupnpp opposite da (MN2+)
3SQ0: “DNA POLYMERASE(L561A/S565G/Y567A) ternary complex with dupnpp opposite da (MN2+)”. X-ray diffraction, 2 ligands (DUP, MN), 11 pockets (best druggability 0.81). MolNFT v1 #78987 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3SQ0
- Type
- protein + DNA
- Length
- 934 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase; 5'-D(*TP*CP*AP*AP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G) -3'…
- EC
- 2.7.7.7
- UniProt
- Q38087
- Ligands
- DUP, MN
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase (EC 2.7.7.7) | protein | 903 | 44% helix, 19% strand | Q38087 |
| T | 5'-D(*TP*CP*AP*AP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G) -3' | dna | 18 | — | — |
| P | 5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*(DOC))-3' | dna | 13 | — | — |
Ligands and binding sites
- DUP · 2'-deoxyuridine 5'-alpha,beta-imido-triphosphate · ligand · chains A, T, P
- MN · Manganese (II) ion · metal · 5 copies · chains A, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 385 | 0.81 | 0.90 | 38 | empty |
| 2 | 873 | 0.78 | 0.81 | 77 | MN |
| 3 | 621 | 0.76 | 0.82 | 63 | DUP, MN |
| 4 | 521 | 0.75 | 0.83 | 51 | empty |
| 5 | 124 | 0.56 | 0.83 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1232 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–P · 643 Ų buried · 12 hydrogen bonds · protein-nucleic
- T–P · 585 Ų buried · 50 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3SQ0 · DNA Polymerase(L561A/S565G/Y567A) Ternary Complex with dUpNpp Opposite dA (Mn2+) · the same entry in another collection · chain A against A, TM-score 1.00
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 Q38087
- Elsewhere: RCSB PDB 3SQ0 · PDBe 3SQ0 · UniProt Q38087
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