Research workbench
Crystal structure of E. COLI 3-methyladenine DNA glycosylase (alka) complexed with DNA
Analyse Crystal structure of E. COLI 3-methyladenine DNA glycosylase (alka) complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DIZ
- Type
- protein + DNA
- Length
- 616 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*GP*AP*CP*AP*TP*GP*AP*(NRI)P*TP*GP*CP*CP*T)-3'); DNA…
- EC
- 3.2.2.21
- UniProt
- P04395
- Ligands
- NA
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, E | DNA (5'-D(*GP*AP*CP*AP*TP*GP*AP*(NRI)P*TP*GP*CP*CP*T)-3') | dna | 13 | — | — |
| D, F | DNA (5'-D(*GP*GP*CP*AP*AP*TP*CP*AP*TP*GP*TP*CP*A)-3') | dna | 13 | — | — |
| A, B | 3-methyladenine DNA glycosylase II (EC 3.2.2.21) | protein | 282 | 47% helix, 11% strand | P04395 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains E, A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1165 | 0.84 | 0.84 | 118 | empty |
| 2 | 160 | 0.68 | 0.88 | 24 | empty |
| 3 | 173 | 0.67 | 0.86 | 26 | empty |
| 4 | 98 | 0.48 | 0.81 | 18 | empty |
| 5 | 85 | 0.48 | 0.82 | 17 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1061 Ų buried · 13 hydrogen bonds · protein-protein
- C–B · 602 Ų buried · 14 hydrogen bonds · protein-nucleic
- E–A · 600 Ų buried · 17 hydrogen bonds · protein-nucleic
- E–F · 562 Ų buried · 41 hydrogen bonds · nucleic-nucleic
- C–D · 557 Ų buried · 38 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 1DIZ · Crystal structure of E. COLI 3-methyladenine DNA glycosylase (alka) complexed with DNA · the same entry in another collection · chain B against B, TM-score 1.00
- P04395 · AlphaFold monomer V2.0 prediction for DNA-3-methyladenine glycosylase 2 (P04395) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P04395
- Elsewhere: RCSB PDB 1DIZ · PDBe 1DIZ · UniProt P04395
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