Research workbench
Crystal structure of the BS69 coiled coil-mynd domains bound to an EBNA2 pxlxp motif
Analyse Crystal structure of the BS69 coiled coil-mynd domains bound to an EBNA2 pxlxp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HDA
- Type
- protein
- Length
- 255 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Zinc finger mynd domain-containing protein 11; Epstein-barr nuclear antigen 2
- UniProt
- Q15326, P12978
- Ligands
- ZN
- Pockets
- 1 · best druggability 0.24
Structure
x-ray diffraction · 4 distinct chains · 69% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Zinc finger mynd domain-containing protein 11 | protein | 121 | 74% helix, 8% strand | Q15326 |
| C | Zinc finger mynd domain-containing protein 11 | protein | 117 | 74% helix, 9% strand | Q15326 |
| B | Epstein-barr nuclear antigen 2 | protein | 8 | 0% helix, 13% strand | P12978 |
| D | Epstein-barr nuclear antigen 2 | protein | 9 | 0% helix, 11% strand | P12978 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.24 | 0.72 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–C · 2425 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 429 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 418 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 92 Ų buried · 0 hydrogen bonds · protein-protein
- C–B · 74 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5HDA · Crystal Structure of the BS69 coiled coil-MYND domains bound to an EBNA2 PXLXP motif · the same entry in another collection · chain A against A, TM-score 1.00
- Q15326 · AlphaFold monomer V2.0 prediction for zinc finger mynd domain- containing protein 11… · a predicted model of the same protein · chain C against A, TM-score 0.88
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 Q15326
- Every structure of UniProt P12978
- Elsewhere: RCSB PDB 5HDA · PDBe 5HDA · UniProt Q15326 · UniProt P12978
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