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Crystal structure of T4 pyrimidine dimer glycosylase (T4-pdg) covalently complexed with a DNA substrate containing abasic site
Analyse Crystal structure of T4 pyrimidine dimer glycosylase (T4-pdg) covalently… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FCC
- Type
- protein + DNA
- Length
- 326 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*CP*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3'); DNA…
- EC
- 3.1.25.1
- UniProt
- P04418
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, E | DNA (5'-D(*CP*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3') | dna | 13 | — | — |
| D, F | DNA (5'-D(*GP*GP*CP*(BRU)P*(BRU)P*CP*AP*(BRU)P*CP*CP*(BRU) P*GP*G)-3') | dna | 13 | — | — |
| A, B | Endonuclease V (EC 3.1.25.1) | protein | 137 | 48% helix, 3% strand | P04418 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 121 | 0.66 | 0.90 | 20 | empty |
| 2 | 174 | 0.60 | 0.83 | 20 | empty |
| 3 | 66 | 0.48 | 0.85 | 15 | empty |
Interfaces
6 interfaces between chains.
- E–B · 719 Ų buried · 20 hydrogen bonds · protein-nucleic
- C–A · 701 Ų buried · 20 hydrogen bonds · protein-nucleic
- F–B · 654 Ų buried · 12 hydrogen bonds · protein-nucleic
- D–A · 652 Ų buried · 11 hydrogen bonds · protein-nucleic
- C–D · 552 Ų buried · 52 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 10 modified (nucleotide modification).
Compared structures
- 2FCC · Crystal Structure of T4 Pyrimidine Dimer Glycosylase (T4-Pdg) Covalently Complexed with a… · the same entry in another collection · chain C against C, 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 P04418
- Elsewhere: RCSB PDB 2FCC · PDBe 2FCC · UniProt P04418
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