Research workbench
Crystal structure of human wd repeat domain 5 with compound mm-402
Analyse Crystal structure of human wd repeat domain 5 with compound mm-402 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GMB
- Type
- protein
- Length
- 310 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wd repeat-containing protein 5; Mm-402
- UniProt
- P61964
- Ligands
- ALQ, 0XQ
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Wd repeat-containing protein 5 | protein | 307 | 0% helix, 50% strand | P61964 |
| E | Mm-402 | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- ALQ · 2-methyl-propionic acid · ligand · chains A, E
- 0XQ · (2R)-2,8-diamino-2-methyloctanoic acid · ligand · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 511 | 0.75 | 0.83 | 45 | empty |
| 2 | 53 | 0.56 | 0.90 | 15 | empty |
| 3 | 64 | 0.35 | 0.77 | 15 | ALQ, 0XQ |
Interfaces
1 interface between chains.
- A–E · 360 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, nonstandard).
Compared structures
- 4GMB · Crystal structure of human WD repeat domain 5 with compound MM-402 · the same entry in another collection · chain A against A, 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 P61964
- Elsewhere: RCSB PDB 4GMB · PDBe 4GMB · UniProt P61964
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