MolNFT v1 · #87951 · protein
Crystal structure of the trimerization domain of EML2
4CGB · Echinoderm microtubule-associated protein-like 2: “Crystal structure of the trimerization domain of EML2”. X-ray diffraction, 1 ligand (K), 4 pockets (best druggability 0.35). MolNFT v1 #87951 on GenesisL1: 3D structure, binding…
- PDB
- 4CGB
- Type
- protein
- Length
- 259 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Echinoderm microtubule-associated protein-like 2
- UniProt
- O95834
- Ligands
- K
- Pockets
- 4 · best druggability 0.35
Structure
x-ray diffraction · 5 distinct chains · 93% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Echinoderm microtubule-associated protein-like 2 | protein | 44 | 93% helix, 0% strand | O95834 |
| B | Echinoderm microtubule-associated protein-like 2 | protein | 45 | 96% helix, 0% strand | O95834 |
| C | Echinoderm microtubule-associated protein-like 2 | protein | 41 | 93% helix, 0% strand | O95834 |
| D, F | Echinoderm microtubule-associated protein-like 2 | protein | 45 | 89% helix, 0% strand | O95834 |
| E | Echinoderm microtubule-associated protein-like 2 | protein | 39 | 95% helix, 0% strand | O95834 |
Ligands and binding sites
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 | 98 | 0.35 | 0.74 | 17 | GOL |
| 2 | 104 | 0.34 | 0.73 | 20 | empty |
| 3 | 51 | 0.33 | 0.78 | 10 | empty |
| 4 | 64 | 0.29 | 0.73 | 15 | empty |
Interfaces
10 interfaces between chains.
- D–F · 919 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 906 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 870 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 860 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 845 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4CGB · Crystal structure of the trimerization domain of EML2 · the same entry in another collection · chain F against F, TM-score 1.00
- O95834 · AlphaFold monomer V2.0 prediction for echinoderm microtubule- associated protein-like 2… · a predicted model of the same protein · chain F against A, TM-score 0.29
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 O95834
- Elsewhere: RCSB PDB 4CGB · PDBe 4CGB · UniProt O95834
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