Research workbench
Crystal structure of a replicative DNA polymerase bound to the oxidized guanine lesion guanidinohydantoin
Analyse Crystal structure of a replicative DNA polymerase bound to the oxidized guanine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3L8B
- Type
- protein + DNA
- Length
- 1,850 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase; DNA (5'-D(*AP*C*TP*(G35) P*TP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')…
- EC
- 2.7.7.7
- UniProt
- Q38087
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase (EC 2.7.7.7) | protein | 896 | 45% helix, 18% strand | Q38087 |
| B | DNA polymerase (EC 2.7.7.7) | protein | 896 | 44% helix, 18% strand | Q38087 |
| C, E | DNA (5'-D(*AP*C*TP*(G35) P*TP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3') | dna | 16 | — | — |
| D, F | DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*A)-3') | dna | 13 | — | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 268 | 0.83 | 0.95 | 30 | empty |
| 2 | 272 | 0.83 | 0.94 | 30 | empty |
| 3 | 1024 | 0.74 | 0.77 | 67 | empty |
| 4 | 751 | 0.73 | 0.79 | 54 | empty |
| 5 | 721 | 0.69 | 0.76 | 72 | empty |
Interfaces
7 interfaces between chains.
- B–E · 1062 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–C · 1061 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–D · 718 Ų buried · 21 hydrogen bonds · protein-nucleic
- B–F · 708 Ų buried · 20 hydrogen bonds · protein-nucleic
- E–F · 584 Ų buried · 50 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3L8B · Crystal structure of a replicative DNA polymerase bound to the oxidized guanine lesion… · 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 Q38087
- Elsewhere: RCSB PDB 3L8B · PDBe 3L8B · UniProt Q38087
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