Research workbench
Pseudomonas fluorescens alkylpurine DNA glycosylase alkc bound to DNA containing an abasic site analog
Analyse Pseudomonas fluorescens alkylpurine DNA glycosylase alkc bound to DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VI0
- Type
- protein + DNA
- Length
- 760 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alkylpurine DNA glycosylase alkc; DNA (5'-D(*TP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*T)-3')…
- UniProt
- C3K795
- Ligands
- P4K, NA
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alkylpurine DNA glycosylase alkc | protein | 357 | 49% helix, 22% strand | C3K795 |
| B | Alkylpurine DNA glycosylase alkc | protein | 359 | 47% helix, 22% strand | C3K795 |
| C, F | DNA (5'-D(*TP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*T)-3') | dna | 11 | — | — |
| D, E | DNA (5'-D(*AP*AP*GP*AP*CP*TP*TP*GP*GP*AP*C)-3') | dna | 11 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 408 | 0.79 | 0.88 | 46 | empty |
| 2 | 1042 | 0.77 | 0.80 | 71 | empty |
| 3 | 319 | 0.67 | 0.82 | 25 | empty |
| 4 | 320 | 0.56 | 0.76 | 25 | P4K |
| 5 | 149 | 0.55 | 0.81 | 23 | empty |
Interfaces
7 interfaces between chains.
- B–D · 886 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–E · 690 Ų buried · 9 hydrogen bonds · protein-nucleic
- B–C · 542 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–F · 502 Ų buried · 9 hydrogen bonds · protein-nucleic
- E–F · 474 Ų buried · 35 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 18 modified (engineered, nucleotide modification).
Compared structures
- 5VI0 · Pseudomonas fluorescens alkylpurine DNA glycosylase AlkC bound to DNA containing an… · 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 C3K795
- Elsewhere: RCSB PDB 5VI0 · PDBe 5VI0 · UniProt C3K795
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