MolNFT v1 · #123377 · protein

Crystal structure of GDF8

5JI1 · GROWTH/DIFFERENTIATION factor 8: “Crystal structure of GDF8”. X-ray diffraction, 1 pocket (best druggability 0.31). MolNFT v1 #123377 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5JI1
Type: protein
Length: 187 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GROWTH/DIFFERENTIATION factor 8
UniProt: O08689
Pockets: 1 · best druggability 0.31

Structure

x-ray diffraction · 2 distinct chains · 4% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	GROWTH/DIFFERENTIATION factor 8	protein	95	4% helix, 52% strand	O08689
B	GROWTH/DIFFERENTIATION factor 8	protein	92	4% helix, 53% strand	O08689

Ligands and binding sites

MPD · (4S)-2-methyl-2,4-pentanediol · additive · 7 copies · chains A, B

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	56	0.31	0.76	19	empty

Interfaces

1 interface between chains.

A–B · 648 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide (disulfide).

Compared structures

5JI1 · Crystal Structure of GDF8 · the same entry in another collection · chain A against A, TM-score 1.00
O08689 · AlphaFold monomer V2.0 prediction for GROWTH/DIFFERENTIATION factor 8 (O08689) · a predicted model of the same protein · chain B against A, TM-score 0.89

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 O08689
Elsewhere: RCSB PDB 5JI1 · PDBe 5JI1 · UniProt O08689

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