Research workbench
MBD3 mbd in complex with methylated, non-palindromic cpg DNA: alternative interpretation of crystallographic data
Analyse MBD3 mbd in complex with methylated, non-palindromic cpg DNA: alternative… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CEV
- Type
- protein + DNA
- Length
- 189 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyl-cpg-binding domain protein 3; DNA (5'-D(*GP*CP*CP*AP*GP*(5CM)P*GP*TP*TP*GP*GP*C)-3'…
- UniProt
- O95983
- Ligands
- UNX
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methyl-cpg-binding domain protein 3 | protein | 71 | 11% helix, 32% strand | O95983 |
| B | Methyl-cpg-binding domain protein 3 | protein | 70 | 11% helix, 33% strand | O95983 |
| C, E | DNA (5'-D(*GP*CP*CP*AP*GP*(5CM)P*GP*TP*TP*GP*GP*C)-3') | dna | 12 | — | — |
| D, F | DNA (5'-D(*GP*CP*CP*AP*AP*(5CM)P*GP*CP*TP*GP*GP*C)-3') | dna | 12 | — | — |
Ligands and binding sites
- UNX · Unknown atom or ion · ion · 4 copies · chains A, C, D, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 251 | 0.60 | 0.80 | 40 | empty |
| 2 | 183 | 0.58 | 0.81 | 25 | empty |
| 3 | 121 | 0.42 | 0.76 | 23 | UNX |
Interfaces
7 interfaces between chains.
- C–D · 560 Ų buried · 60 hydrogen bonds · nucleic-nucleic
- E–F · 558 Ų buried · 55 hydrogen bonds · nucleic-nucleic
- A–D · 338 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–F · 317 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–C · 280 Ų buried · 3 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 6CEV · MBD3 MBD in complex with methylated, non-palindromic CpG DNA: alternative interpretation… · the same entry in another collection · chain F against F, TM-score 1.00
- O95983 · AlphaFold monomer V2.0 prediction for methyl-cpg-binding domain protein 3 (O95983) · a predicted model of the same protein · chain B 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 O95983
- Elsewhere: RCSB PDB 6CEV · PDBe 6CEV · UniProt O95983
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