MolNFT v1 · #60033 · protein + DNA
Structure of the replicating complex of a pol alpha family DNA polymerase, ternary complex 2
3CFR · DNA (5'- D(*DTP*DCP*DAP*DAP*DGP*DTP*DAP*DAP*DGP*DCP*DAP*DGP*…: “Structure of the replicating complex of a pol alpha family DNA polymerase, ternary complex 2”. X-ray diffraction, 3 ligands (TTP, CA, CL), 10 pockets (best druggability…
- PDB
- 3CFR
- Type
- protein + DNA
- Length
- 932 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*DTP*DCP*DAP*DAP*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, CL
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | DNA (5'- D(*DTP*DCP*DAP*DAP*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*(DOC))-3') | dna | 13 | — | — |
| A | DNA polymerase (EC 2.7.7.7) | protein | 901 | 43% helix, 17% strand | Q38087 |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · chains T, P, A
- CA · Calcium ion · metal · 5 copies · chains A, P
- CL · Chloride ion · ion · 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 | 291 | 0.84 | 0.95 | 33 | empty |
| 2 | 845 | 0.81 | 0.84 | 85 | empty |
| 3 | 613 | 0.77 | 0.83 | 66 | CA, CL, TTP |
| 4 | 420 | 0.65 | 0.78 | 43 | empty |
| 5 | 110 | 0.58 | 0.85 | 18 | empty |
Interfaces
3 interfaces between chains.
- T–A · 1368 Ų buried · 22 hydrogen bonds · protein-nucleic
- P–A · 694 Ų buried · 15 hydrogen bonds · protein-nucleic
- T–P · 595 Ų buried · 66 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3CFR · Structure of the replicating complex of a POL Alpha family DNA Polymerase, ternary… · 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 3CFR · PDBe 3CFR · UniProt Q38087
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