MolNFT v2 · #220797 · protein

Cryo-EM Structure of GPR61-

8TB7 · G-protein coupled receptor 61,Soluble cytochrome b562: “Cryo-EM Structure of GPR61-”. Electron microscopy at 2.94, 1 ligand (ZOB), 8 pockets (best druggability 0.72). MolNFT v2 #220797 on GenesisL1: 3D structure, binding sites and…

PDB: 8TB7
Type: protein
Length: 879 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.94
Source: Escherichia coli; Homo sapiens; Lama glama
Molecule: G-protein coupled receptor 61,Soluble cytochrome b562; Fab24 BAK5 heavy chain; Fab…
UniProt: Q9BZJ8, P0ABE7
Ligands: ZOB
Pockets: 8 · best druggability 0.72

Structure

electron microscopy · resolution 2.94 · 4 distinct chains · 32% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
R	G-protein coupled receptor 61,Soluble cytochrome b562	protein	328	77% helix, 0% strand	Q9BZJ8, P0ABE7
H	Fab24 BAK5 heavy chain	protein	222	5% helix, 50% strand	—
N	Fab hinge-binding nanobody	protein	117	3% helix, 42% strand	—
L	Fab24 BAK5 light chain	protein	212	6% helix, 48% strand	—

Ligands and binding sites

ZOB · 6-{[(3,5-difluoropyridin-4-yl)methyl]amino}-N-(4-ethoxy-6-methylpyrimidin-2-yl)-2-methoxy-N-(2-methoxyethyl)pyridine-3-sulfonamide · ligand · chains R

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

Pockets

8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	582	0.72	0.80	57	ZOB
2	397	0.57	0.74	56	empty
3	181	0.53	0.78	27	empty
4	64	0.53	0.87	19	empty
5	239	0.52	0.76	31	empty

Interfaces

4 interfaces between chains.

H–L · 1886 Å² buried · 6 hydrogen bonds · protein-protein
N–L · 686 Å² buried · 11 hydrogen bonds · protein-protein
R–L · 435 Å² buried · 2 hydrogen bonds · protein-protein
R–H · 297 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain R against A, TM-score 0.35

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 Q9BZJ8
Every structure of UniProt P0ABE7
Elsewhere: RCSB PDB 8TB7 · PDBe 8TB7 · UniProt Q9BZJ8 · UniProt P0ABE7

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