MolNFT v1 · #115415 · protein + DNA
Structural basis of the recognition of H3K36ME3 by DNMT3B pwwp domain
5CIY · Modification methylase hhai: “Structural basis of the recognition of H3K36ME3 by DNMT3B pwwp domain”. X-ray diffraction, 2 ligands (SAH, SO4), 5 pockets (best druggability 0.72). MolNFT v1 #115415 on GenesisL1: 3D structure, binding…
- PDB
- 5CIY
- Type
- protein + DNA
- Length
- 351 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Modification methylase hhai; DNA (5'-D(P*CP*CP*AP*TP*GP*CP*GP*CP*TP*GP*AP*C)-3'); DNA…
- EC
- 2.1.1.37
- UniProt
- P05102
- Ligands
- SAH, SO4
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Modification methylase hhai (EC 2.1.1.37) | protein | 327 | 34% helix, 19% strand | P05102 |
| C | DNA (5'-D(P*CP*CP*AP*TP*GP*CP*GP*CP*TP*GP*AP*C)-3') | dna | 12 | — | — |
| D | DNA (5'-D(P*GP*TP*CP*AP*GP*(3DR)P*GP*CP*AP*TP*GP*G)-3') | dna | 12 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 242 | 0.72 | 0.87 | 35 | SAH |
| 2 | 54 | 0.71 | 0.99 | 24 | empty |
| 3 | 203 | 0.55 | 0.79 | 22 | empty |
| 4 | 141 | 0.53 | 0.81 | 16 | empty |
| 5 | 66 | 0.29 | 0.74 | 11 | empty |
Interfaces
3 interfaces between chains.
- A–D · 918 Ų buried · 24 hydrogen bonds · protein-nucleic
- A–C · 729 Ų buried · 12 hydrogen bonds · protein-nucleic
- C–D · 550 Ų buried · 41 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 5CIY · Structural basis of the recognition of H3K36me3 by DNMT3B PWWP domain · the same entry in another collection · chain A against A, TM-score 1.00
- P05102 · AlphaFold monomer V2.0 prediction for modification methylase hhai (P05102) · 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 P05102
- Elsewhere: RCSB PDB 5CIY · PDBe 5CIY · UniProt P05102
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