Research workbench
Cereblon isoform 4 from magnetospirillum gryphiswaldense in multiple conformations, hexagonal crystal form
Analyse Cereblon isoform 4 from magnetospirillum gryphiswaldense in multiple… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AMK
- Type
- protein
- Length
- 422 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cereblon isoform 4
- UniProt
- A4TVL0
- Ligands
- EF2, ZN
- Pockets
- 5 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Cereblon isoform 4 | protein | 105 | 6% helix, 50% strand | A4TVL0 |
| D | Cereblon isoform 4 | protein | 107 | 6% helix, 45% strand | A4TVL0 |
Ligands and binding sites
- EF2 · S-Thalidomide · ligand · 2 copies · chains A, B, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 202 | 0.56 | 0.79 | 39 | EF2 |
| 2 | 89 | 0.45 | 0.80 | 21 | empty |
| 3 | 84 | 0.41 | 0.79 | 20 | EF2 |
| 4 | 87 | 0.35 | 0.75 | 19 | empty |
| 5 | 53 | 0.32 | 0.77 | 13 | empty |
Interfaces
5 interfaces between chains.
- A–D · 721 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 688 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 550 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 341 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 149 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5AMK · Cereblon isoform 4 from Magnetospirillum gryphiswaldense in multiple conformations… · the same entry in another collection · chain B against B, 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 A4TVL0
- Elsewhere: RCSB PDB 5AMK · PDBe 5AMK · UniProt A4TVL0
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