Research workbench
Crystal structure of the VPS33-VPS16 hops subcomplex from chaetomium thermophilum
Analyse Crystal structure of the VPS33-VPS16 hops subcomplex from chaetomium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KMO
- Type
- protein
- Length
- 839 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Small conjugating protein ligase-like protein; Putative vacuolar protein…
- Ligands
- SO4
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Small conjugating protein ligase-like protein | protein | 574 | 48% helix, 16% strand | — |
| B | Putative vacuolar protein sorting-associated protein | protein | 265 | 64% helix, 0% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 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 | 0.79 | 0.82 | 84 | SO4 |
| 2 | 402 | 0.67 | 0.79 | 43 | empty |
| 3 | 167 | 0.57 | 0.81 | 29 | empty |
| 4 | 228 | 0.48 | 0.74 | 32 | empty |
| 5 | 104 | 0.44 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2412 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 4KMO · Crystal Structure of the Vps33-Vps16 HOPS subcomplex from Chaetomium thermophilum · 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
- Elsewhere: RCSB PDB 4KMO · PDBe 4KMO
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