Research workbench
Bacillus DNA polymerase I large fragment complex 1
Analyse Bacillus DNA polymerase I large fragment complex 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EZ6
- Type
- protein + DNA
- Length
- 1,170 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*(DDG))-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q5KWC1
- Ligands
- DG3, SO4
- Pockets
- 17 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 54% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase (EC 2.7.7.7) | protein | 549 | 54% helix, 14% strand | Q5KWC1 |
| D | DNA polymerase (EC 2.7.7.7) | protein | 580 | 54% helix, 14% strand | Q5KWC1 |
| B, E | DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DDG))-3') | dna | 9 | — | — |
| C | DNA (5'-D(*CP*AP*TP*GP*CP*GP*AP*GP*TP*CP*AP*GP*G)-3') | dna | 11 | — | — |
| F | DNA (5'-D(*CP*AP*TP*GP*CP*GP*AP*GP*TP*CP*AP*GP*G)-3') | dna | 12 | — | — |
Ligands and binding sites
- DG3 · 2'-3'-dideoxyguanosine-5'-triphosphate · ligand · 2 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · chains 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
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 967 | 0.76 | 0.79 | 63 | DG3 |
| 2 | 909 | 0.76 | 0.79 | 76 | DG3 |
| 3 | 525 | 0.72 | 0.81 | 51 | empty |
| 4 | 333 | 0.67 | 0.82 | 42 | empty |
| 5 | 310 | 0.67 | 0.82 | 45 | empty |
Interfaces
7 interfaces between chains.
- D–F · 1208 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–C · 1156 Ų buried · 25 hydrogen bonds · protein-nucleic
- D–E · 840 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–B · 839 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–D · 709 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 4EZ6 · Bacillus DNA Polymerase I Large Fragment Complex 1 · 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 4EZ6 · PDBe 4EZ6 · UniProt Q5KWC1
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