Research workbench
Crystal structure of HMCES cross-linked to DNA abasic site
Analyse Crystal structure of HMCES cross-linked to DNA abasic site in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OE7
- Type
- protein + DNA
- Length
- 273 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.2
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Embryonic stem cell-specific 5-hydroxymethylcytosine-binding protein; DNA…
- UniProt
- Q96FZ2
- Ligands
- UNX
- Pockets
- 5 · best druggability 0.41
Structure
x-ray diffraction · resolution 2.2 · 3 distinct chains · 23% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Embryonic stem cell-specific 5-hydroxymethylcytosine-binding protein | protein | 258 | 23% helix, 31% strand | Q96FZ2 |
| C | DNA (5'-D(*GP*TP*CP*TP*GP*G)-3') | dna | 6 | — | — |
| B | DNA (5'-D(*CP*CP*AP*GP*AP*CP*GP*TP*(DRZ)P*GP*TP*T)-3') | dna | 9 | — | — |
Ligands and binding sites
- UNX · Unknown atom or ion · ion · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 60 | 0.41 | 0.81 | 15 | EDO |
| 2 | 60 | 0.40 | 0.80 | 15 | EDO |
| 3 | 64 | 0.34 | 0.77 | 14 | EDO |
| 4 | 74 | 0.30 | 0.73 | 15 | empty |
| 5 | 56 | 0.27 | 0.73 | 11 | UNX |
Interfaces
3 interfaces between chains.
- A–B · 629 Ų buried · 19 hydrogen bonds · protein-nucleic
- C–B · 274 Ų buried · 29 hydrogen bonds · nucleic-nucleic
- A–C · 215 Ų buried · 1 hydrogen bond · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6OE7 · Crystal structure of hmces cross-linked to DNA abasic site · the same entry in another collection · chain A against A, TM-score 1.00
- Q96FZ2 · AlphaFold monomer V2.0 prediction for abasic site processing protein hmces (Q96FZ2) · 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 Q96FZ2
- Elsewhere: RCSB PDB 6OE7 · PDBe 6OE7 · UniProt Q96FZ2
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