MolNFT v1 · #60388 · protein + DNA
Ternary complex of the L415F mutant RB69 exo(-)polymerase
3CQ8 · DNA (5'- D(*DAP*DCP*DAP*DGP*DGP*DTP*DAP*DAP*DGP*DCP*DAP*DGP*…: “Ternary complex of the L415F mutant RB69 exo(-)polymerase”. X-ray diffraction, 3 ligands (TTP, CA, NA), 10 pockets (best druggability 0.84). MolNFT v1 #60388 on…
- PDB
- 3CQ8
- Type
- protein + DNA
- Length
- 934 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*DAP*DCP*DAP*DGP*DGP*DTP*DAP*DAP*DGP*DCP*DAP*DGP*DTP*DCP*DCP*DGP*DC P*DG)-3')…
- EC
- 2.7.7.7
- UniProt
- Q38087
- Ligands
- TTP, CA, NA
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | DNA (5'- D(*DAP*DCP*DAP*DGP*DGP*DTP*DAP*DAP*DGP*DCP*DAP*DGP*DTP*DCP*DCP*DGP*DC P*DG)-3') | dna | 18 | — | — |
| P | DNA (5'- D(*DGP*DCP*DGP*DGP*DAP*DCP*DTP*DGP*DCP*DTP*DTP*DAP*DCP*DC)-3') | dna | 14 | — | — |
| A | DNA polymerase (EC 2.7.7.7) | protein | 902 | 42% helix, 18% strand | Q38087 |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · chains T, P, A
- CA · Calcium ion · metal · 6 copies · chains A
- NA · Sodium ion · metal · 3 copies · chains A
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 314 | 0.84 | 0.94 | 32 | empty |
| 2 | 1105 | 0.76 | 0.79 | 76 | CA |
| 3 | 878 | 0.76 | 0.80 | 72 | CA, TTP |
| 4 | 508 | 0.63 | 0.76 | 44 | empty |
| 5 | 129 | 0.59 | 0.84 | 21 | empty |
Interfaces
3 interfaces between chains.
- T–A · 1156 Ų buried · 16 hydrogen bonds · protein-nucleic
- P–A · 697 Ų buried · 14 hydrogen bonds · protein-nucleic
- T–P · 623 Ų buried · 59 hydrogen bonds · nucleic-nucleic
Compared structures
- 3CQ8 · Ternary complex of the L415F mutant RB69 exo(-)polymerase · 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 3CQ8 · PDBe 3CQ8 · UniProt Q38087
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