MolNFT v1 · #120083 · protein

Truncated mitofusin-1, transition-like state

5GOM: “Truncated mitofusin-1, transition-like state”. X-ray diffraction, 1 ligand (GDP), 7 pockets (best druggability 0.82). MolNFT v1 #120083 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5GOM
Type: protein
Length: 811 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mitofusin-1
EC: 3.6.5.-
UniProt: Q8IWA4
Ligands: GDP
Pockets: 7 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 58% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Mitofusin-1 (EC 3.6.5.-)	protein	407	57% helix, 12% strand	Q8IWA4
B	Mitofusin-1 (EC 3.6.5.-)	protein	404	59% helix, 11% strand	Q8IWA4

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1054	0.82	0.83	118	GDP
2	126	0.43	0.77	19	empty
3	82	0.36	0.76	17	empty
4	65	0.31	0.75	17	empty
5	83	0.30	0.73	17	empty

Interfaces

1 interface between chains.

A–B · 1122 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

5GOM · Truncated mitofusin-1, transition-like state · the same entry in another collection · chain A against A, TM-score 1.00
Q8IWA4 · AlphaFold monomer V2.0 prediction for mitofusin-1 (Q8IWA4) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q8IWA4
Elsewhere: RCSB PDB 5GOM · PDBe 5GOM · UniProt Q8IWA4

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