Research workbench
Bacillus cereus DNA glycosylase alkd bound to 7-methylguanine nucleobase and DNA containing an oxocarbenium-intermediate analog
Analyse Bacillus cereus DNA glycosylase alkd bound to 7-methylguanine nucleobase and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KUB
- Type
- protein + DNA
- Length
- 255 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-7-methylguanine glycosylase; DNA (5'-D(*CP*CP*CP*GP*AP*(NRI)P*AP*GP*TP*CP*CP*G)-3')…
- EC
- 3.2.2.-
- UniProt
- C2T7T7
- Ligands
- MY6
- Pockets
- 1 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 72% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-7-methylguanine glycosylase (EC 3.2.2.-) | protein | 231 | 72% helix, 1% strand | C2T7T7 |
| B | DNA (5'-D(*CP*CP*CP*GP*AP*(NRI)P*AP*GP*TP*CP*CP*G)-3') | dna | 12 | — | — |
| C | DNA (5'-D(*CP*GP*GP*AP*CP*TP*CP*TP*CP*GP*GP*G)-3') | dna | 12 | — | — |
Ligands and binding sites
- MY6 · 2-amino-7-methyl-1,7-dihydro-6H-purin-6-one · ligand · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1069 | 0.79 | 0.81 | 62 | MY6 |
Interfaces
3 interfaces between chains.
- B–C · 541 Ų buried · 48 hydrogen bonds · nucleic-nucleic
- A–B · 501 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–C · 300 Ų buried · 9 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 5KUB · Bacillus cereus DNA glycosylase AlkD bound to 7-methylguanine nucleobase and DNA… · 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 C2T7T7
- Elsewhere: RCSB PDB 5KUB · PDBe 5KUB · UniProt C2T7T7
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