MolNFT v1 · #145425 · protein + DNA
Crystal structure of MBD2 complex with methylated cpg island
6CNP · Methyl-cpg-binding domain protein 2: “Crystal structure of MBD2 complex with methylated cpg island”. X-ray diffraction, 2 ligands (CA, UNX), 5 pockets (best druggability 0.56). MolNFT v1 #145425 on GenesisL1: 3D structure, binding…
- PDB
- 6CNP
- Type
- protein + DNA
- Length
- 174 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyl-cpg-binding domain protein 2; DNA (5'-D(*GP*CP*CP*AP*CP*(5CM)P*GP*GP*TP*GP*GP*C)-3'…
- UniProt
- Q9UBB5
- Ligands
- CA, UNX
- Pockets
- 5 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 13% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methyl-cpg-binding domain protein 2 | protein | 68 | 12% helix, 29% strand | Q9UBB5 |
| B | Methyl-cpg-binding domain protein 2 | protein | 58 | 14% helix, 24% strand | Q9UBB5 |
| C, D, E, F | DNA (5'-D(*GP*CP*CP*AP*CP*(5CM)P*GP*GP*TP*GP*GP*C)-3') | dna | 12 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · chains A
- UNX · Unknown atom or ion · ion · 11 copies · chains A, B, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 192 | 0.56 | 0.80 | 22 | empty |
| 2 | 166 | 0.53 | 0.80 | 23 | UNX |
| 3 | 202 | 0.43 | 0.73 | 20 | UNX |
| 4 | 136 | 0.40 | 0.74 | 14 | empty |
| 5 | 76 | 0.30 | 0.74 | 15 | UNX |
Interfaces
8 interfaces between chains.
- E–F · 574 Ų buried · 59 hydrogen bonds · nucleic-nucleic
- C–D · 567 Ų buried · 54 hydrogen bonds · nucleic-nucleic
- A–C · 345 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–E · 342 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–F · 319 Ų buried · 5 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 6CNP · Crystal structure of MBD2 complex with methylated CpG island · the same entry in another collection · chain F against F, TM-score 1.00
- Q9UBB5 · AlphaFold monomer V2.0 prediction for methyl-cpg-binding domain protein 2 (Q9UBB5) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 6CNP · PDBe 6CNP · UniProt Q9UBB5
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