Research workbench
Complex of MBD1-mbd and methylated DNA
Analyse Complex of MBD1-mbd and methylated DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D1T
- Type
- protein + DNA
- Length
- 92 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyl-cpg-binding domain protein 1; DNA (5'-D(*GP*CP*CP*AP*AP*(5CM)P*GP*TP*TP*GP*GP*C)-3'…
- UniProt
- Q9UIS9
- Ligands
- UNX
- Pockets
- 2 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methyl-cpg-binding domain protein 1 | protein | 68 | 12% helix, 26% strand | Q9UIS9 |
| B, C | DNA (5'-D(*GP*CP*CP*AP*AP*(5CM)P*GP*TP*TP*GP*GP*C)-3') | dna | 12 | — | — |
Ligands and binding sites
- UNX · Unknown atom or ion · ion · 12 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 93 | 0.63 | 0.90 | 20 | UNX |
| 2 | 124 | 0.46 | 0.78 | 19 | UNX |
Interfaces
3 interfaces between chains.
- B–C · 537 Ų buried · 48 hydrogen bonds · nucleic-nucleic
- A–B · 360 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–C · 348 Ų buried · 5 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
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 Q9UIS9
- Elsewhere: RCSB PDB 6D1T · PDBe 6D1T · UniProt Q9UIS9
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