Research workbench
Mutant cereblon isoform 4 from magnetospirillum gryphiswaldense in complex with thalidomide metabolite alpha-(O-carboxybenzamido) glutarimide
Analyse Mutant cereblon isoform 4 from magnetospirillum gryphiswaldense in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6R0Q
- Type
- protein
- Length
- 435 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cereblon isoform 4; Ala-ala-ala; Ala-ala-ala-ala
- UniProt
- A4TVL0
- Ligands
- JNW, ZN
- Pockets
- 8 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cereblon isoform 4 | protein | 107 | 6% helix, 50% strand | A4TVL0 |
| B, D | Cereblon isoform 4 | protein | 104 | 6% helix, 55% strand | A4TVL0 |
| F, E, G | Ala-ala-ala | protein | 3 | 0% helix, 33% strand | — |
| H | Ala-ala-ala-ala | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- JNW · 2-[[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]carbamoyl]benzoic acid · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 230 | 0.63 | 0.82 | 29 | JNW |
| 2 | 211 | 0.62 | 0.82 | 32 | JNW |
| 3 | 210 | 0.59 | 0.81 | 30 | JNW |
| 4 | 207 | 0.59 | 0.81 | 31 | JNW |
| 5 | 202 | 0.53 | 0.78 | 32 | empty |
Interfaces
10 interfaces between chains.
- C–D · 691 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 687 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 432 Ų buried · 0 hydrogen bonds · protein-protein
- A–F · 142 Ų buried · 3 hydrogen bonds · protein-protein
- C–E · 142 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6R0Q · Mutant cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with… · 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 6R0Q · PDBe 6R0Q · UniProt A4TVL0
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