Research workbench
Cryo-EM structure of the C2-symmetric TRPV2/RTX complex in amphipol resolved to 3.3 a
Analyse Cryo-EM structure of the C2-symmetric TRPV2/RTX complex in amphipol resolved to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OO4
- Type
- protein
- Length
- 2,440 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRPV2
- UniProt
- G1SNM3
- Ligands
- 6EU
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 55% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | TRPV2 | protein | 610 | 55% helix, 6% strand | G1SNM3 |
Ligands and binding sites
- 6EU · resiniferatoxin · ligand · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1173 | 0.84 | 0.84 | 93 | empty |
| 2 | 616 | 0.83 | 0.87 | 52 | empty |
| 3 | 576 | 0.82 | 0.87 | 49 | empty |
| 4 | 908 | 0.82 | 0.83 | 94 | empty |
| 5 | 729 | 0.81 | 0.85 | 51 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2621 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 2608 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 2604 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 2603 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 23 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6OO4 · Cryo-EM structure of the C2-symmetric TRPV2/RTx complex in amphipol resolved to 3.3 A · 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 G1SNM3
- Elsewhere: RCSB PDB 6OO4 · PDBe 6OO4 · UniProt G1SNM3
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