MolNFT v1 · #160847 · protein

Cryo-EM structure of thermo-sensitive TRP channel TRP1 from the alga chlamydomonas reinhardtii in nanodiscs

6PW5 · TRP-like ion channel: “Cryo-EM structure of thermo-sensitive TRP channel TRP1 from the alga chlamydomonas reinhardtii in nanodiscs”. Electron microscopy, 3 ligands (PIO, PCW, PIK), 20 pockets (best druggability 0.88). MolNFT v1…

PDB: 6PW5
Type: protein
Length: 3,032 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TRP-like ion channel
UniProt: Q0Z852
Ligands: PIO, PCW, PIK
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 2 distinct chains · 56% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	TRP-like ion channel	protein	734	56% helix, 0% strand	Q0Z852
B, D	TRP-like ion channel	protein	782	56% helix, 1% strand	Q0Z852

Ligands and binding sites

PIO · [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2, 3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate · ligand · 4 copies · chains A, D, B, C
PCW · 1,2-dioleoyl-sn-glycero-3-phosphocholine · ligand · 4 copies · chains A, D, B, C
PIK · (2S)-3-{[(R)-hydroxy{[(1r,2r,3s,4r,5r,6s)-2,3,6-trihydroxy-4,5-bis(phosphonooxy) cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dihexadecanoate · 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	935	0.88	0.90	126	empty
2	1116	0.85	0.86	144	empty
3	1115	0.85	0.86	140	empty
4	1045	0.84	0.85	113	PIK
5	950	0.78	0.80	74	PIO, PCW

Interfaces

6 interfaces between chains.

B–C · 5018 Å² buried · 38 hydrogen bonds · protein-protein
A–D · 4996 Å² buried · 38 hydrogen bonds · protein-protein
C–D · 4661 Å² buried · 30 hydrogen bonds · protein-protein
A–B · 4650 Å² buried · 30 hydrogen bonds · protein-protein
B–D · 257 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent, 4 disulfide (covalent ligand, disulfide).

Compared structures

6PW5 · Cryo-EM Structure of Thermo-Sensitive TRP Channel TRP1 from the Alga Chlamydomonas… · 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 Q0Z852
Elsewhere: RCSB PDB 6PW5 · PDBe 6PW5 · UniProt Q0Z852

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