MolNFT v1 · #137439 · protein

Crystal structure of the C7ORF59-hbxip dimer

5VOK · Ragulator complex protein LAMTOR5: “Crystal structure of the C7ORF59-hbxip dimer”. X-ray diffraction, 10 pockets (best druggability 0.61). MolNFT v1 #137439 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5VOK
Type: protein
Length: 705 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ragulator complex protein LAMTOR5; Ragulator complex protein LAMTOR4
UniProt: O43504, Q0VGL1
Pockets: 10 · best druggability 0.61

Structure

x-ray diffraction · 5 distinct chains · 19% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Ragulator complex protein LAMTOR5	protein	90	23% helix, 20% strand	O43504
B, F	Ragulator complex protein LAMTOR4	protein	93	15% helix, 35% strand	Q0VGL1
C, G	Ragulator complex protein LAMTOR5	protein	88	24% helix, 33% strand	O43504
D	Ragulator complex protein LAMTOR4	protein	83	18% helix, 35% strand	Q0VGL1
H	Ragulator complex protein LAMTOR4	protein	80	15% helix, 43% strand	Q0VGL1

Pockets

10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	427	0.61	0.76	50	empty
2	50	0.55	0.90	16	empty
3	275	0.54	0.75	27	empty
4	115	0.47	0.79	18	empty
5	104	0.45	0.79	20	empty

Interfaces

11 interfaces between chains.

A–B · 997 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 969 Å² buried · 17 hydrogen bonds · protein-protein
E–F · 943 Å² buried · 10 hydrogen bonds · protein-protein
G–H · 856 Å² buried · 15 hydrogen bonds · protein-protein
E–G · 415 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5VOK · Crystal structure of the C7orf59-HBXIP dimer · the same entry in another collection · chain H against H, TM-score 1.00
O43504 · AlphaFold monomer V2.0 prediction for ragulator complex protein LAMTOR5 (O43504) · a predicted model of the same protein · chain C against A, TM-score 0.95
Q0VGL1 · AlphaFold monomer V2.0 prediction for ragulator complex protein LAMTOR4 (Q0VGL1) · a predicted model of the same protein · chain D against A, TM-score 0.83

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 O43504
Every structure of UniProt Q0VGL1
Elsewhere: RCSB PDB 5VOK · PDBe 5VOK · UniProt O43504 · UniProt Q0VGL1

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