MolNFT v1 · #91081 · protein + DNA
DNA polymerase I large fragment complex 3
4F2R: “DNA polymerase I large fragment complex 3”. X-ray diffraction, 5 ligands (CTP, GLC, FRU), 16 pockets (best druggability 0.73). MolNFT v1 #91081 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4F2R
- Type
- protein + DNA
- Length
- 1,202 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase; DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q5KWC1
- Ligands
- CTP, GLC, FRU, MG, SO4
- Pockets
- 16 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 55% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase (EC 2.7.7.7) | protein | 578 | 56% helix, 13% strand | Q5KWC1 |
| D | DNA polymerase (EC 2.7.7.7) | protein | 583 | 54% helix, 13% strand | Q5KWC1 |
| B, E | DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3') | dna | 9 | — | — |
| C | DNA (5'-D(*CP*AP*TP*GP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3') | dna | 11 | — | — |
| F | DNA (5'-D(*CP*AP*TP*GP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3') | dna | 12 | — | — |
Ligands and binding sites
- CTP · Cytidine-5'-triphosphate · ligand · 2 copies · chains A, B, C, D, E, F
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, D
- FRU · beta-D-fructofuranose · sugar · 2 copies · chains A, D
- MG · Magnesium ion · metal · chains D
- SO4 · Sulfate ion · ion · 3 copies · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 693 | 0.73 | 0.79 | 54 | empty |
| 2 | 1123 | 0.71 | 0.75 | 74 | CTP, MG |
| 3 | 1044 | 0.71 | 0.75 | 67 | CTP |
| 4 | 393 | 0.70 | 0.82 | 45 | GLC, FRU |
| 5 | 351 | 0.68 | 0.81 | 44 | GLC, FRU |
Interfaces
7 interfaces between chains.
- A–C · 1204 Ų buried · 24 hydrogen bonds · protein-nucleic
- D–F · 1200 Ų buried · 27 hydrogen bonds · protein-nucleic
- D–E · 797 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–B · 778 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–D · 731 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 4F2R · DNA Polymerase I Large Fragment complex 3 · 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 Q5KWC1
- Elsewhere: RCSB PDB 4F2R · PDBe 4F2R · UniProt Q5KWC1
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