MolNFT v1 · #78915 · protein + DNA
RB69 DNA polymerase (L561A/S565G/Y567A) ternary complex with dctp opposite dg in the presence of MG2+
3SNN · 5'-D(*TP*CP*AP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)…: “RB69 DNA polymerase (L561A/S565G/Y567A) ternary complex with dctp opposite dg in the presence of MG2+”. X-ray diffraction, 2 ligands (DCP, MG), 11 pockets (best…
- PDB
- 3SNN
- Type
- protein + DNA
- Length
- 934 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*TP*CP*AP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G) -3'…
- EC
- 2.7.7.7
- UniProt
- Q38087
- Ligands
- DCP, MG
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | 5'-D(*TP*CP*AP*GP*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 | — | — |
| A | DNA polymerase (EC 2.7.7.7) | protein | 903 | 44% helix, 19% strand | Q38087 |
Ligands and binding sites
- DCP · 2'-deoxycytidine-5'-triphosphate · ligand · chains T, P, A
- MG · Magnesium ion · metal · 2 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 302 | 0.82 | 0.93 | 35 | empty |
| 2 | 393 | 0.77 | 0.87 | 52 | DCP, MG |
| 3 | 266 | 0.71 | 0.86 | 41 | empty |
| 4 | 398 | 0.63 | 0.78 | 42 | empty |
| 5 | 110 | 0.58 | 0.85 | 19 | empty |
Interfaces
3 interfaces between chains.
- T–A · 1341 Ų buried · 26 hydrogen bonds · protein-nucleic
- P–A · 660 Ų buried · 14 hydrogen bonds · protein-nucleic
- T–P · 613 Ų buried · 62 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3SNN · RB69 DNA Polymerase (L561A/S565G/Y567A) Ternary Complex with dCTP Opposite dG in the… · the same entry in another collection · chain T against T, 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 3SNN · PDBe 3SNN · UniProt Q38087
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