Research workbench
Pseudomonas fluorescens alkylpurine DNA glycosylase alkc bound to DNA containing an oxocarbenium-intermediate 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
- 5VHV
- Type
- protein + DNA
- Length
- 766 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*(NRI)P*GP*TP*CP*T)-3')…
- UniProt
- C3K795
- Ligands
- 9B4, NA
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alkylpurine DNA glycosylase alkc | protein | 361 | 47% helix, 20% strand | C3K795 |
| C, E | DNA (5'-D(*TP*GP*TP*CP*CP*AP*(NRI)P*GP*TP*CP*T)-3') | dna | 11 | — | — |
| D, F | DNA (5'-D(*AP*AP*GP*AP*CP*TP*TP*GP*GP*AP*C)-3') | dna | 11 | — | — |
Ligands and binding sites
- 9B4 · (2R,5R,13R,16R)-9-(hydroxymethyl)-9-{[(2R)-2-hydroxypropoxy]methyl}-5,13-dimethyl-4,7,11,14-tetraoxaheptadecane-2,16-diol · ligand · 2 copies · chains A, C, D, B, E, F
- NA · Sodium ion · metal · 2 copies · chains C, D, E, F
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 3 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, C, D, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 809 | 0.78 | 0.81 | 66 | empty |
| 2 | 452 | 0.76 | 0.85 | 38 | empty |
| 3 | 532 | 0.73 | 0.82 | 44 | empty |
| 4 | 311 | 0.71 | 0.85 | 23 | 9B4 |
| 5 | 259 | 0.70 | 0.86 | 34 | empty |
Interfaces
7 interfaces between chains.
- A–B · 799 Ų buried · 10 hydrogen bonds · protein-protein
- B–F · 755 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–D · 754 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–E · 593 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–C · 574 Ų buried · 15 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 5VHV · 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 5VHV · PDBe 5VHV · UniProt C3K795
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