MolNFT v1 · #117810 · protein

Crystal structural of the TSC1-TBC1D7 complex

5EJC · TBC1 domain family member 7: “Crystal structural of the TSC1-TBC1D7 complex”. X-ray diffraction, 6 pockets (best druggability 0.46). MolNFT v1 #117810 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5EJC
Type: protein
Length: 671 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TBC1 domain family member 7; Hamartin
UniProt: Q9P0N9, Q92574
Pockets: 6 · best druggability 0.46

Structure

x-ray diffraction · 6 distinct chains · 72% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	TBC1 domain family member 7	protein	268	67% helix, 1% strand	Q9P0N9
B	TBC1 domain family member 7	protein	267	67% helix, 1% strand	Q9P0N9
C	Hamartin	protein	31	94% helix, 0% strand	Q92574
D	Hamartin	protein	34	91% helix, 0% strand	Q92574
E	Hamartin	protein	32	91% helix, 0% strand	Q92574
F	Hamartin	protein	39	90% helix, 0% strand	Q92574

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	136	0.46	0.77	28	empty
2	106	0.45	0.79	21	empty
3	60	0.36	0.78	14	empty
4	64	0.35	0.77	15	empty
5	85	0.34	0.75	22	empty

Interfaces

10 interfaces between chains.

E–F · 1016 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 971 Å² buried · 6 hydrogen bonds · protein-protein
A–E · 820 Å² buried · 9 hydrogen bonds · protein-protein
B–D · 801 Å² buried · 6 hydrogen bonds · protein-protein
C–F · 543 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 modified (engineered).

Compared structures

5EJC · Crystal structural of the TSC1-TBC1D7 complex · the same entry in another collection · chain F against F, TM-score 1.00
Q9P0N9 · AlphaFold monomer V2.0 prediction for TBC1 domain family member 7 (Q9P0N9) · a predicted model of the same protein · chain B against A, TM-score 1.00
Q92574 · AlphaFold monomer V2.0 prediction for hamartin (Q92574) · a predicted model of the same protein · chain E against A, TM-score 0.91

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 Q9P0N9
Every structure of UniProt Q92574
Elsewhere: RCSB PDB 5EJC · PDBe 5EJC · UniProt Q9P0N9 · UniProt Q92574

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