MolNFT v1 · #114617 · protein
Crystal structure of a complex between the snare NYV1 and the hops VPS33-VPS16 subcomplex from chaetomium thermophilum
5BV0 · Sm (SEC1/MUNC18-like) protein: “Crystal structure of a complex between the snare NYV1 and the hops VPS33-VPS16 subcomplex from chaetomium…”. X-ray diffraction, 13 pockets (best druggability 0.79). MolNFT v1 #114617 on GenesisL1: 3D…
- PDB
- 5BV0
- Type
- protein
- Length
- 846 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sm (SEC1/MUNC18-like) protein; VPS16; Snare domain
- UniProt
- G0SCM5, G0S5G3
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sm (SEC1/MUNC18-like) protein | protein | 604 | 48% helix, 15% strand | G0SCM5 |
| B | VPS16 | protein | 207 | 69% helix, 0% strand | — |
| C | Snare domain | protein | 35 | 69% helix, 0% strand | G0S5G3 |
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 757 | 0.79 | 0.83 | 78 | empty |
| 2 | 53 | 0.71 | 0.99 | 19 | empty |
| 3 | 567 | 0.70 | 0.79 | 65 | empty |
| 4 | 397 | 0.66 | 0.79 | 37 | empty |
| 5 | 131 | 0.54 | 0.82 | 22 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2483 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1140 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5BV0 · Crystal Structure of a Complex Between the SNARE Nyv1 and the HOPS Vps33-Vps16 subcomplex… · 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 G0S5G3
- Elsewhere: RCSB PDB 5BV0 · PDBe 5BV0 · UniProt G0SCM5 · UniProt G0S5G3
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