Research workbench
Crystal structure of the merlin FERM/DCAF1 complex
Analyse Crystal structure of the merlin FERM/DCAF1 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4P7I
- Type
- protein
- Length
- 608 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Merlin; Protein vprbp
- EC
- 2.7.11.1
- UniProt
- P46662, Q9Y4B6
- Pockets
- 13 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Merlin | protein | 294 | 37% helix, 26% strand | P46662 |
| B | Merlin | protein | 292 | 36% helix, 23% strand | P46662 |
| C | Protein vprbp (EC 2.7.11.1) | protein | 15 | 0% helix, 67% strand | Q9Y4B6 |
| D | Protein vprbp (EC 2.7.11.1) | protein | 7 | 0% helix, 57% strand | Q9Y4B6 |
Ligands and binding sites
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 774 | 0.73 | 0.78 | 62 | empty |
| 2 | 330 | 0.62 | 0.78 | 32 | empty |
| 3 | 249 | 0.58 | 0.78 | 27 | empty |
| 4 | 174 | 0.46 | 0.75 | 18 | empty |
| 5 | 125 | 0.46 | 0.78 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–C · 625 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 429 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 429 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4P7I · Crystal structure of the Merlin FERM/DCAF1 complex · the same entry in another collection · chain D against D, TM-score 1.00
- P46662 · AlphaFold monomer V2.0 prediction for merlin (P46662) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q9Y4B6 · AlphaFold monomer V2.0 prediction for DDB1- and CUL4-associated factor 1 (Q9Y4B6) · a predicted model of the same protein · chain D against A, TM-score 0.69
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 P46662
- Every structure of UniProt Q9Y4B6
- Elsewhere: RCSB PDB 4P7I · PDBe 4P7I · UniProt P46662 · UniProt Q9Y4B6
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