MolNFT v1 · #92888 · protein
Crystal structure of human wd repeat domain 5 with compound mm-102
4GM8 · Wd repeat-containing protein 5: “Crystal structure of human wd repeat domain 5 with compound mm-102”. X-ray diffraction, 3 ligands (ALQ, 0XL, 0XN), 11 pockets (best druggability 0.83). MolNFT v1 #92888 on GenesisL1: 3D structure…
- PDB
- 4GM8
- Type
- protein
- Length
- 1,212 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wd repeat-containing protein 5; Mm-102
- UniProt
- P61964
- Ligands
- ALQ, 0XL, 0XN
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 0% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Wd repeat-containing protein 5 | protein | 302 | 0% helix, 52% strand | P61964 |
| B | Wd repeat-containing protein 5 | protein | 300 | 0% helix, 52% strand | P61964 |
| D | Wd repeat-containing protein 5 | protein | 300 | 0% helix, 52% strand | P61964 |
| E, F, G, H | Mm-102 | protein | 2 | 0% helix, 0% strand | — |
Ligands and binding sites
- ALQ · 2-methyl-propionic acid · ligand · 4 copies · chains A, E, B, F, C, G, D, H
- 0XL · 2-amino-2-ethylbutanoic acid · ligand · 4 copies · chains A, E, B, F, C, G, D, H
- 0XN · 1,1-bis(4-fluorophenyl)methanamine · ligand · 4 copies · chains A, E, B, F, C, G, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 947 | 0.83 | 0.84 | 87 | empty |
| 2 | 974 | 0.82 | 0.84 | 88 | empty |
| 3 | 476 | 0.73 | 0.82 | 44 | empty |
| 4 | 468 | 0.73 | 0.82 | 44 | empty |
| 5 | 155 | 0.49 | 0.78 | 25 | empty |
Interfaces
7 interfaces between chains.
- B–C · 664 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 409 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 402 Ų buried · 2 hydrogen bonds · protein-protein
- A–E · 310 Ų buried · 4 hydrogen bonds · protein-protein
- B–F · 307 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent, 4 modified (covalent ligand, nonstandard).
Compared structures
- 4GM8 · Crystal structure of human WD repeat domain 5 with compound MM-102 · 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 4GM8 · PDBe 4GM8 · UniProt P61964
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