Research workbench
Structure of MBOGG1 in complex with high affinity DNA ligand
Analyse Structure of MBOGG1 in complex with high affinity DNA ligand in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EJY
- Type
- protein + DNA
- Length
- 640 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-methyladenine DNA glycosylase; DNA (5'-D(*AP*GP*CP*GP*TP*CP*CP*AP*(3DR)…
- EC
- 3.2.2.-
- UniProt
- Q8R5T9
- Ligands
- NA
- Pockets
- 13 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-methyladenine DNA glycosylase (EC 3.2.2.-) | protein | 289 | 50% helix, 13% strand | Q8R5T9 |
| B | 3-methyladenine DNA glycosylase (EC 3.2.2.-) | protein | 289 | 49% helix, 13% strand | Q8R5T9 |
| C, E | DNA (5'-D(*AP*GP*CP*GP*TP*CP*CP*AP*(3DR) P*GP*TP*CP*TP*AP*CP*C)-3') | dna | 16 | — | — |
| D, F | DNA (5'-D(*T*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)- 3') | dna | 15 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, C, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 804 | 0.71 | 0.77 | 62 | empty |
| 2 | 87 | 0.71 | 0.95 | 22 | empty |
| 3 | 181 | 0.68 | 0.87 | 33 | empty |
| 4 | 248 | 0.48 | 0.73 | 28 | empty |
| 5 | 124 | 0.40 | 0.75 | 17 | empty |
Interfaces
9 interfaces between chains.
- E–F · 680 Ų buried · 60 hydrogen bonds · nucleic-nucleic
- A–C · 667 Ų buried · 15 hydrogen bonds · protein-nucleic
- C–D · 664 Ų buried · 63 hydrogen bonds · nucleic-nucleic
- B–E · 642 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–D · 398 Ų buried · 8 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 4EJY · Structure of MBOgg1 in complex with high affinity DNA ligand · 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 Q8R5T9
- Elsewhere: RCSB PDB 4EJY · PDBe 4EJY · UniProt Q8R5T9
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