MolNFT v1 · #145440 · protein
Structure of the NVTRPM2 channel in complex with CA2+
6CO7 · Predicted protein: “Structure of the NVTRPM2 channel in complex with CA2+”. Electron microscopy, 5 ligands (POV, CLR, NAG), 20 pockets (best druggability 0.87). MolNFT v1 #145440 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6CO7
- Type
- protein
- Length
- 4,244 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Predicted protein
- UniProt
- A7T1N0
- Ligands
- POV, CLR, NAG, CA, NA
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 1 distinct chain · 57% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Predicted protein | protein | 1061 | 57% helix, 6% strand | A7T1N0 |
Ligands and binding sites
- POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · 56 copies · chains A, B, D, C
- CLR · Cholesterol · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 3 copies · chains A, B, C, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 969 | 0.87 | 0.89 | 80 | NA |
| 2 | 1052 | 0.82 | 0.83 | 93 | POV |
| 3 | 722 | 0.82 | 0.86 | 77 | empty |
| 4 | 854 | 0.82 | 0.84 | 85 | empty |
| 5 | 1074 | 0.82 | 0.82 | 94 | POV |
Interfaces
6 interfaces between chains.
- A–D · 4864 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 4856 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 4856 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 4849 Ų buried · 31 hydrogen bonds · protein-protein
- B–D · 72 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan (N-glycosylation).
Compared structures
- 6CO7 · Structure of the nvTRPM2 channel in complex with Ca2+ · the same entry in another collection · chain A against A, TM-score 1.00
- A7T1N0 · AlphaFold monomer V2.0 prediction for transient receptor potential cation channel… · a predicted model of the same protein · chain A against A, TM-score 0.92
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 A7T1N0
- Elsewhere: RCSB PDB 6CO7 · PDBe 6CO7 · UniProt A7T1N0
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