MolNFT v2 · #226216 · protein

ExoC110T class 1 channelrhodopsin

8ZAP · C110T-class1: “ExoC110T class 1 channelrhodopsin”. Electron microscopy at 2.6, 2 ligands (RET, K), 10 pockets (best druggability 0.85). MolNFT v2 #226216 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 8ZAP
Type: protein
Length: 776 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.6
Source: Hyphochytrium catenoides
Molecule: C110T-class1
Ligands: RET, K
Pockets: 10 · best druggability 0.85

Structure

electron microscopy · resolution 2.6 · 2 distinct chains · 68% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	C110T-class1	protein	258	67% helix, 2% strand	—
B, C	C110T-class1	protein	259	68% helix, 2% strand	—

Ligands and binding sites

RET · Retinal · ligand · 3 copies · chains A, B, C
K · Potassium ion · metal · 24 copies · chains A, B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	987	0.85	0.86	108	K
2	148	0.81	0.97	23	RET
3	158	0.81	0.96	27	RET
4	144	0.80	0.97	25	RET
5	232	0.57	0.78	28	empty

Interfaces

3 interfaces between chains.

A–C · 1147 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 1146 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 1095 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 cofactor (retinal Schiff base).

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 8ZAP · PDBe 8ZAP

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