Research workbench
The crystal structure of methyl-cpg binding domain of human MECP2 in complex with a methylated DNA sequence from bdnf
Analyse The crystal structure of methyl-cpg binding domain of human MECP2 in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3C2I
- Type
- protein + DNA
- Length
- 112 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyl-cpg-binding protein 2; DNA (5'-D(*DTP*DCP*DTP*DGP*DGP*DAP*DAP*(5CM)…
- UniProt
- P51608
- Pockets
- 3 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methyl-cpg-binding protein 2 | protein | 72 | 15% helix, 19% strand | P51608 |
| B | DNA (5'-D(*DTP*DCP*DTP*DGP*DGP*DAP*DAP*(5CM) P*DGP*DGP*DAP*DAP*DTP*DTP*DCP*DTP*DTP*DCP*DTP*DA)-3') | dna | 20 | — | — |
| C | DNA (5'- D(*DAP*DTP*DAP*DGP*DAP*DAP*DGP*DAP*DAP*DTP*DTP*DCP*(5CM) P*DGP*DTP*DTP*DCP*DCP*DAP*DG)-3') | dna | 20 | — | — |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 173 | 0.58 | 0.82 | 29 | empty |
| 2 | 178 | 0.47 | 0.76 | 19 | empty |
| 3 | 52 | 0.24 | 0.73 | 11 | empty |
Interfaces
3 interfaces between chains.
- B–C · 894 Ų buried · 98 hydrogen bonds · nucleic-nucleic
- A–B · 379 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–C · 349 Ų buried · 5 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified (engineered, nucleotide modification).
Compared structures
- 3C2I · The Crystal Structure of Methyl-CpG Binding Domain of Human MeCP2 in Complex with a… · the same entry in another collection · chain A against A, TM-score 1.00
- 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 0.90
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 3C2I · PDBe 3C2I · UniProt P51608
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