MolNFT v1 · #78986 · protein + DNA
DNA POLYMERASE(L415A/L561A/S565G/Y567A) ternary complex with dupcpp opposite da (CA2+)
3SPZ: “DNA POLYMERASE(L415A/L561A/S565G/Y567A) ternary complex with dupcpp opposite da (CA2+)”. X-ray diffraction, 2 ligands (UPC, CA), 12 pockets (best druggability 0.83). MolNFT v1 #78986 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3SPZ
- Type
- protein + DNA
- Length
- 932 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase; 5'-D(P*GP*AP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3'…
- EC
- 2.7.7.7
- UniProt
- Q38087
- Ligands
- UPC, CA
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase (EC 2.7.7.7) | protein | 903 | 44% helix, 18% strand | Q38087 |
| T | 5'-D(P*GP*AP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3' | dna | 16 | — | — |
| P | 5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*C)-3' | dna | 13 | — | — |
Ligands and binding sites
- UPC · 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]uridine · ligand · chains A, T, P
- CA · Calcium ion · metal · 4 copies · chains A, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 320 | 0.83 | 0.93 | 36 | empty |
| 2 | 1130 | 0.78 | 0.80 | 74 | CA |
| 3 | 1024 | 0.77 | 0.79 | 92 | UPC, CA |
| 4 | 406 | 0.63 | 0.78 | 33 | empty |
| 5 | 130 | 0.56 | 0.83 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1066 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–P · 654 Ų buried · 14 hydrogen bonds · protein-nucleic
- T–P · 587 Ų buried · 55 hydrogen bonds · nucleic-nucleic
Compared structures
- 3SPZ · DNA Polymerase(L415A/L561A/S565G/Y567A) Ternary Complex with dUpCpp Opposite dA (Ca2+) · 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 3SPZ · PDBe 3SPZ · UniProt Q38087
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