Research workbench
Crystal structure of chaetomium thermophilum VPS29
Analyse Crystal structure of chaetomium thermophilum VPS29 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W8M
- Type
- protein
- Length
- 1,141 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vacuolar protein sorting-associated protein 29
- UniProt
- G0RZB5
- Pockets
- 17 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 14% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vacuolar protein sorting-associated protein 29 | protein | 196 | 14% helix, 36% strand | G0RZB5 |
| B | Vacuolar protein sorting-associated protein 29 | protein | 189 | 14% helix, 37% strand | G0RZB5 |
| C | Vacuolar protein sorting-associated protein 29 | protein | 189 | 14% helix, 36% strand | G0RZB5 |
| D | Vacuolar protein sorting-associated protein 29 | protein | 195 | 14% helix, 37% strand | G0RZB5 |
| E | Vacuolar protein sorting-associated protein 29 | protein | 187 | 13% helix, 39% strand | G0RZB5 |
| F | Vacuolar protein sorting-associated protein 29 | protein | 185 | 15% helix, 37% strand | G0RZB5 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 993 | 0.79 | 0.80 | 81 | empty |
| 2 | 559 | 0.69 | 0.79 | 46 | empty |
| 3 | 208 | 0.67 | 0.86 | 33 | empty |
| 4 | 375 | 0.63 | 0.78 | 50 | empty |
| 5 | 120 | 0.63 | 0.87 | 22 | empty |
Interfaces
9 interfaces between chains.
- E–F · 763 Ų buried · 15 hydrogen bonds · protein-protein
- D–F · 727 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 700 Ų buried · 8 hydrogen bonds · protein-protein
- C–E · 679 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 609 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5W8M · Crystal structure of Chaetomium thermophilum Vps29 · 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 G0RZB5
- Elsewhere: RCSB PDB 5W8M · PDBe 5W8M · UniProt G0RZB5
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