Research workbench
Crystal structure of a VPS33-VPS16 complex from chaetomium thermophilum
Analyse Crystal structure of a VPS33-VPS16 complex from chaetomium thermophilum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BV1
- Type
- protein
- Length
- 1,797 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VPS33; Putative vacuolar protein sorting-associated protein
- UniProt
- G0SCM5, G0S6M7
- Ligands
- MLT
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 53% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VPS33 | protein | 601 | 49% helix, 15% strand | G0SCM5 |
| B, D | Putative vacuolar protein sorting-associated protein | protein | 297 | 68% helix, 0% strand | G0S6M7 |
| C | VPS33 | protein | 602 | 50% helix, 15% strand | G0SCM5 |
Ligands and binding sites
- MLT · D-malate · ligand · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 971 | 0.80 | 0.82 | 105 | MLT |
| 2 | 683 | 0.78 | 0.83 | 71 | empty |
| 3 | 53 | 0.72 | 0.99 | 19 | empty |
| 4 | 342 | 0.65 | 0.80 | 41 | empty |
| 5 | 289 | 0.64 | 0.80 | 35 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2349 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 2315 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 131 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 56 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5BV1 · Crystal Structure of a Vps33-Vps16 Complex 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
- Every structure of UniProt G0SCM5
- Every structure of UniProt G0S6M7
- Elsewhere: RCSB PDB 5BV1 · PDBe 5BV1 · UniProt G0SCM5 · UniProt G0S6M7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.