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Major tropism determinant U1 variant

Analyse Major tropism determinant U1 variant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1YU4
Type: protein
Length: 1,128 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Major tropism determinant (mtd-U1)
UniProt: Q775D6
Ligands: MG
Pockets: 7 · best druggability 0.85

Structure

x-ray diffraction · 1 distinct chain · 11% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Major tropism determinant (mtd-U1)	protein	376	11% helix, 33% strand	Q775D6

Ligands and binding sites

MG · Magnesium ion · metal · 5 copies · chains A, B, C

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

Pockets

7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	615	0.85	0.90	72	MG
2	337	0.81	0.91	32	empty
3	52	0.48	0.86	14	empty
4	54	0.48	0.85	15	empty
5	120	0.38	0.74	21	empty

Interfaces

3 interfaces between chains.

A–C · 2421 Å² buried · 33 hydrogen bonds · protein-protein
B–C · 2378 Å² buried · 32 hydrogen bonds · protein-protein
A–B · 2359 Å² buried · 32 hydrogen bonds · protein-protein

Compared structures

1YU4 · Major Tropism Determinant U1 Variant · the same entry in another collection · chain A against A, TM-score 1.00

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 Q775D6
Elsewhere: RCSB PDB 1YU4 · PDBe 1YU4 · UniProt Q775D6

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