MolNFT v1 · #91114 · protein + DNA
DNA polymerase I large fragment complex 5
4F3O: “DNA polymerase I large fragment complex 5”. X-ray diffraction, 3 ligands (D3T, MN, SO4), 18 pockets (best druggability 0.76). MolNFT v1 #91114 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4F3O
- Type
- protein + DNA
- Length
- 1,187 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*(2DT))-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q5KWC1
- Ligands
- D3T, MN, SO4
- Pockets
- 18 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase (EC 2.7.7.7) | protein | 566 | 54% helix, 13% strand | Q5KWC1 |
| D | DNA polymerase (EC 2.7.7.7) | protein | 579 | 55% helix, 14% strand | Q5KWC1 |
| B, E | DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(2DT))-3') | dna | 9 | — | — |
| C, F | DNA (5'-D(*C*AP*TP*GP*AP*GP*AP*GP*TP*CP*AP*GP*G)-3') | dna | 12 | — | — |
Ligands and binding sites
- D3T · 2',3'-dideoxy-thymidine-5'-triphosphate · ligand · chains D, E, F
- MN · Manganese (II) ion · metal · 2 copies · chains A, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 905 | 0.76 | 0.79 | 68 | D3T, MN |
| 2 | 877 | 0.76 | 0.79 | 65 | MN |
| 3 | 508 | 0.72 | 0.81 | 52 | empty |
| 4 | 307 | 0.69 | 0.83 | 44 | empty |
| 5 | 221 | 0.67 | 0.85 | 28 | empty |
Interfaces
7 interfaces between chains.
- A–C · 1257 Ų buried · 25 hydrogen bonds · protein-nucleic
- D–F · 1214 Ų buried · 22 hydrogen bonds · protein-nucleic
- D–E · 807 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–B · 785 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–D · 715 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 4F3O · DNA Polymerase I Large Fragment Complex 5 · 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 4F3O · PDBe 4F3O · UniProt Q5KWC1
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