Research workbench
Crystal structure of wild type lactococcus lactis fpg complexed to a tetrahydrofuran containing DNA
Analyse Crystal structure of wild type lactococcus lactis fpg complexed to a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PM5
- Type
- protein + DNA
- Length
- 299 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*CP*TP*CP*TP*TP*TP*(3DR)P*TP*TP*TP*CP*TP*CP*G)- 3'); DNA…
- EC
- 3.2.2.23
- UniProt
- P42371
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | DNA (5'-D(*CP*TP*CP*TP*TP*TP*(3DR)P*TP*TP*TP*CP*TP*CP*G)- 3') | dna | 14 | — | — |
| E | DNA (5'-D(*GP*CP*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*A)-3') | dna | 14 | — | — |
| A | Formamidopyrimidine-DNA glycosylase (EC 3.2.2.23) | protein | 271 | 33% helix, 23% strand | P42371 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 701 | 0.73 | 0.79 | 47 | GOL |
| 2 | 298 | 0.65 | 0.81 | 26 | empty |
| 3 | 127 | 0.42 | 0.76 | 21 | GOL |
| 4 | 58 | 0.31 | 0.76 | 16 | empty |
| 5 | 57 | 0.31 | 0.76 | 16 | empty |
Interfaces
3 interfaces between chains.
- D–A · 693 Ų buried · 15 hydrogen bonds · protein-nucleic
- D–E · 538 Ų buried · 35 hydrogen bonds · nucleic-nucleic
- E–A · 419 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 1PM5 · Crystal structure of wild type Lactococcus lactis Fpg complexed to a tetrahydrofuran… · the same entry in another collection · chain D against D, TM-score 1.00
- P42371 · AlphaFold monomer V2.0 prediction for formamidopyrimidine-DNA glycosylase (P42371) · a predicted model of the same protein · 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 P42371
- Elsewhere: RCSB PDB 1PM5 · PDBe 1PM5 · UniProt P42371
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