Research workbench
MBD2 in complex with methylated DNA
Analyse MBD2 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
- 6C2F
- Type
- protein + DNA
- Length
- 552 residues
- Chains
- 18
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyl-cpg-binding domain protein 2; 12-mer DNA
- UniProt
- Q9UBB5
- Ligands
- UNX
- Pockets
- 17 · best druggability 0.57
Structure
x-ray diffraction · 5 distinct chains · 16% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methyl-cpg-binding domain protein 2 | protein | 69 | 16% helix, 30% strand | Q9UBB5 |
| B, E, H, K, N, Q | 12-mer DNA | dna | 12 | — | — |
| C, F, I, L, O, R | 12-mer DNA | dna | 12 | — | — |
| D, G, M, P | Methyl-cpg-binding domain protein 2 | protein | 68 | 16% helix, 32% strand | Q9UBB5 |
| J | Methyl-cpg-binding domain protein 2 | protein | 67 | 16% helix, 31% strand | Q9UBB5 |
Ligands and binding sites
- UNX · Unknown atom or ion · ion · 11 copies · chains A, B, D, G, J, K, M, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 139 | 0.57 | 0.83 | 22 | empty |
| 2 | 99 | 0.56 | 0.85 | 20 | empty |
| 3 | 118 | 0.52 | 0.82 | 20 | empty |
| 4 | 110 | 0.49 | 0.81 | 19 | empty |
| 5 | 101 | 0.49 | 0.82 | 17 | empty |
Interfaces
23 interfaces between chains.
- H–I · 549 Ų buried · 51 hydrogen bonds · nucleic-nucleic
- B–C · 547 Ų buried · 50 hydrogen bonds · nucleic-nucleic
- K–L · 547 Ų buried · 46 hydrogen bonds · nucleic-nucleic
- E–F · 545 Ų buried · 50 hydrogen bonds · nucleic-nucleic
- N–O · 544 Ų buried · 51 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 6 modified (nucleotide modification).
Compared structures
- 6C2F · MBD2 in complex with methylated DNA · the same entry in another collection · chain R against R, 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 Q9UBB5
- Elsewhere: RCSB PDB 6C2F · PDBe 6C2F · UniProt Q9UBB5
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