Research workbench
Human MBD4 glycosylase domain bound to DNA containing oxacarbenium-ion analog 1-aza-2'-deoxyribose
Analyse Human MBD4 glycosylase domain bound to DNA containing oxacarbenium-ion analog… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KZG
- Type
- protein + DNA
- Length
- 168 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyl-cpg-binding domain protein 4; DNA (5'-D(*CP*CP*AP*GP*CP*GP*(NR1)P*GP*CP*AP*GP*C)-3'…
- EC
- 3.2.2.-
- UniProt
- O95243
- Ligands
- NA, CL
- Pockets
- 2 · best druggability 0.41
Structure
x-ray diffraction · 3 distinct chains · 63% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methyl-cpg-binding domain protein 4 (EC 3.2.2.-) | protein | 144 | 63% helix, 0% strand | O95243 |
| C | DNA (5'-D(*CP*CP*AP*GP*CP*GP*(NR1)P*GP*CP*AP*GP*C)-3') | dna | 12 | — | — |
| D | DNA (5'-D(*GP*CP*TP*GP*CP*GP*CP*GP*CP*TP*GP*G)-3') | dna | 12 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · chains A, C
- CL · Chloride ion · ion · chains A, C
- GOL · Glycerol · additive · 4 copies · chains A, C, D
- PEG · Di(hydroxyethyl)ether · additive · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 68 | 0.41 | 0.80 | 16 | GOL |
| 2 | 50 | 0.39 | 0.81 | 13 | GOL, CL |
Interfaces
3 interfaces between chains.
- A–C · 654 Ų buried · 20 hydrogen bonds · protein-nucleic
- C–D · 543 Ų buried · 50 hydrogen bonds · nucleic-nucleic
- A–D · 425 Ų buried · 11 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 7KZG · Human MBD4 glycosylase domain bound to DNA containing oxacarbenium-ion analog… · the same entry in another collection · chain A against A, TM-score 1.00
- O95243 · AlphaFold monomer V2.0 prediction for methyl-cpg-binding domain protein 4 (O95243) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O95243
- Elsewhere: RCSB PDB 7KZG · PDBe 7KZG · UniProt O95243
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