Research workbench
Crystal structure of hmces srap domain in complex with 3' overhang DNA
Analyse Crystal structure of hmces srap domain in complex with 3' overhang DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OEB
- Type
- protein + DNA
- Length
- 272 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Embryonic stem cell-specific 5-hydroxymethylcytosine- binding protein; DNA…
- UniProt
- Q96FZ2
- Ligands
- UNX
- Pockets
- 4 · best druggability 0.41
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Embryonic stem cell-specific 5-hydroxymethylcytosine- binding protein | protein | 257 | 22% helix, 32% strand | Q96FZ2 |
| B | DNA (5'-D(*CP*CP*AP*GP*AP*CP*GP*TP*T)-3') | dna | 9 | — | — |
| C | DNA (5'-D(*GP*TP*CP*TP*GP*G)-3') | dna | 6 | — | — |
Ligands and binding sites
- UNX · Unknown atom or ion · ion · 11 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 69 | 0.41 | 0.80 | 15 | EDO |
| 2 | 111 | 0.40 | 0.76 | 15 | empty |
| 3 | 57 | 0.37 | 0.79 | 13 | EDO |
| 4 | 62 | 0.32 | 0.77 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 609 Ų buried · 16 hydrogen bonds · protein-nucleic
- B–C · 274 Ų buried · 27 hydrogen bonds · nucleic-nucleic
- A–C · 252 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
- 6OEB · Crystal structure of HMCES SRAP domain in complex with 3' overhang DNA · 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 1.00
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 6OEB · PDBe 6OEB · UniProt Q96FZ2
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