MolNFT v1 · #92889 · protein
Crystal structure of human wd repeat domain 5 with compound mm-401
4GM9 · Wd repeat-containing protein 5: “Crystal structure of human wd repeat domain 5 with compound mm-401”. X-ray diffraction, 2 ligands (ALQ, 0XO), 7 pockets (best druggability 0.82). MolNFT v1 #92889 on GenesisL1: 3D structure, binding…
- PDB
- 4GM9
- Type
- protein
- Length
- 625 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wd repeat-containing protein 5; Mm-401
- UniProt
- P61964
- Ligands
- ALQ, 0XO
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 0% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Wd repeat-containing protein 5 | protein | 309 | 0% helix, 50% strand | P61964 |
| B | Wd repeat-containing protein 5 | protein | 310 | 0% helix, 49% strand | P61964 |
| E, F | Mm-401 | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- ALQ · 2-methyl-propionic acid · ligand · 2 copies · chains A, E, B, F
- 0XO · 2-methyl-D-lysine · ligand · 2 copies · chains A, E, B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1112 | 0.82 | 0.82 | 85 | empty |
| 2 | 493 | 0.75 | 0.83 | 46 | empty |
| 3 | 52 | 0.56 | 0.90 | 18 | empty |
| 4 | 277 | 0.55 | 0.76 | 33 | empty |
| 5 | 69 | 0.46 | 0.83 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 785 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 357 Ų buried · 4 hydrogen bonds · protein-protein
- B–F · 346 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 4 modified (covalent ligand, nonstandard).
Compared structures
- 4GM9 · Crystal structure of human WD repeat domain 5 with compound MM-401 · 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 4GM9 · PDBe 4GM9 · UniProt P61964
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