MolNFT v1 · #159095 · protein + DNA
Crystal structure of hmces srap domain in complex with longer 3' overhang DNA
6OEA · Embryonic stem cell-specific 5-hydroxymethylcytosine…: “Crystal structure of hmces srap domain in complex with longer 3' overhang DNA”. X-ray diffraction, 1 ligand (UNX), 4 pockets (best druggability 0.43). MolNFT v1 #159095 on…
- PDB
- 6OEA
- Type
- protein + DNA
- Length
- 274 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…
- EC
- 3.4.-.-
- UniProt
- Q96FZ2
- Ligands
- UNX
- Pockets
- 4 · best druggability 0.43
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Embryonic stem cell-specific 5-hydroxymethylcytosine- binding protein (EC 3.4.-.-) | protein | 258 | 23% helix, 31% strand | Q96FZ2 |
| B | DNA (5'-D(*CP*CP*AP*GP*AP*CP*GP*TP*TP*GP*TP*T)-3') | dna | 10 | — | — |
| 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 · 5 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 | 135 | 0.43 | 0.76 | 20 | empty |
| 2 | 58 | 0.38 | 0.80 | 15 | EDO |
| 3 | 51 | 0.36 | 0.79 | 13 | EDO |
| 4 | 63 | 0.33 | 0.77 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 658 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–C · 276 Ų buried · 27 hydrogen bonds · nucleic-nucleic
- A–C · 248 Ų buried · 1 hydrogen bond · protein-nucleic
Compared structures
- 6OEA · Crystal structure of HMCES SRAP domain in complex with longer 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 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 6OEA · PDBe 6OEA · UniProt Q96FZ2
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