Research workbench
MECP2 mbd domain (A140V) in complex with methylated DNA
Analyse MECP2 mbd domain (A140V) in complex with methylated DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BT2
- Type
- protein + DNA
- Length
- 111 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyl-cpg-binding protein 2; DNA (5'-D(*TP*CP*TP*GP*GP*AP*AP*(5CM)…
- UniProt
- P51608
- Pockets
- 2 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methyl-cpg-binding protein 2 | protein | 71 | 18% helix, 20% strand | P51608 |
| B | DNA (5'-D(*TP*CP*TP*GP*GP*AP*AP*(5CM) P*GP*GP*AP*AP*TP*TP*CP*TP*TP*CP*TP*A)-3') | dna | 20 | — | — |
| C | DNA (5'-D(*AP*TP*AP*GP*AP*AP*GP*AP*AP*TP*TP*CP*(5CM) P*GP*TP*TP*CP*CP*AP*G)-3') | dna | 20 | — | — |
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 | 255 | 0.58 | 0.79 | 41 | empty |
| 2 | 166 | 0.48 | 0.77 | 20 | empty |
Interfaces
3 interfaces between chains.
- B–C · 865 Ų buried · 73 hydrogen bonds · nucleic-nucleic
- A–B · 373 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–C · 344 Ų buried · 5 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- P51608 · AlphaFold monomer V2.0 prediction for methyl-cpg-binding protein 2 (P51608) · a predicted model of the same protein · chain A against A, TM-score 0.91
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 P51608
- Elsewhere: RCSB PDB 5BT2 · PDBe 5BT2 · UniProt P51608
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.