MolNFT v1 · #190764 · protein

Human GDAP1 core domain, trigonal crystal form

7YWD · Ganglioside-induced differentiation-associated protein 1: “Human GDAP1 core domain, trigonal crystal form”. X-ray diffraction, 14 pockets (best druggability 0.80). MolNFT v1 #190764 on GenesisL1: 3D structure, binding sites and…

PDB: 7YWD
Type: protein
Length: 994 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ganglioside-induced differentiation-associated protein 1
UniProt: Q8TB36
Pockets: 14 · best druggability 0.80

Structure

x-ray diffraction · 4 distinct chains · 57% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ganglioside-induced differentiation-associated protein 1	protein	243	55% helix, 9% strand	Q8TB36
B	Ganglioside-induced differentiation-associated protein 1	protein	245	60% helix, 8% strand	Q8TB36
C	Ganglioside-induced differentiation-associated protein 1	protein	248	56% helix, 9% strand	Q8TB36
D	Ganglioside-induced differentiation-associated protein 1	protein	258	57% helix, 9% strand	Q8TB36

Pockets

14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1190	0.80	0.81	112	empty
2	143	0.63	0.86	21	empty
3	298	0.56	0.76	28	empty
4	115	0.52	0.82	25	empty
5	165	0.52	0.79	30	empty

Interfaces

3 interfaces between chains.

A–B · 747 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 739 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 717 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

7YWD · Human GDAP1 core domain, trigonal crystal form · the same entry in another collection · chain D against D, TM-score 1.00
Q8TB36 · AlphaFold monomer V2.0 prediction for ganglioside-induced differentiation-associated… · 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 Q8TB36
Elsewhere: RCSB PDB 7YWD · PDBe 7YWD · UniProt Q8TB36

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