Research workbench
Crystal structure of human wd repeat domain 5 with compound mm-101
Analyse Crystal structure of human wd repeat domain 5 with compound mm-101 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GM3
- Type
- protein
- Length
- 2,448 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wd repeat-containing protein 5; Mm-101
- UniProt
- P61964
- Ligands
- ALQ, 0XL, 0XM
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Wd repeat-containing protein 5 | protein | 304 | 0% helix, 52% strand | P61964 |
| I, J, K, L, M, N, O, P | Mm-101 | protein | 2 | 0% helix, 0% strand | — |
Ligands and binding sites
- ALQ · 2-methyl-propionic acid · ligand · 8 copies · chains A, I, B, J, C, K, D, L, E, H, M, F, N, G, O, P
- 0XL · 2-amino-2-ethylbutanoic acid · ligand · 8 copies · chains A, I, B, J, C, K, D, L, E, H, M, F, N, G, O, P
- 0XM · 1,1-diphenylmethanamine · ligand · 8 copies · chains A, I, B, J, C, K, D, L, E, H, M, F, N, G, O, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 939 | 0.82 | 0.84 | 78 | empty |
| 2 | 901 | 0.82 | 0.84 | 77 | empty |
| 3 | 840 | 0.82 | 0.84 | 74 | empty |
| 4 | 1059 | 0.76 | 0.78 | 66 | ALQ, 0XL, 0XM |
| 5 | 427 | 0.71 | 0.82 | 30 | empty |
Interfaces
17 interfaces between chains.
- F–G · 780 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 758 Ų buried · 10 hydrogen bonds · protein-protein
- E–H · 635 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 560 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 458 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 covalent, 8 modified (covalent ligand, nonstandard).
Compared structures
- 4GM3 · Crystal structure of human WD repeat domain 5 with compound MM-101 · 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 4GM3 · PDBe 4GM3 · UniProt P61964
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