MolNFT v1 · #137225 · protein + DNA
Pseudomonas fluorescens alkylpurine DNA glycosylase alkc bound to DNA containing an abasic site analog
5VI0: “Pseudomonas fluorescens alkylpurine DNA glycosylase alkc bound to DNA containing an abasic site analog”. X-ray diffraction, 2 ligands (P4K, NA), 10 pockets (best druggability 0.79). MolNFT v1 #137225 on GenesisL1: 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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