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Crystal structure of LIP5 N-terminal domain

Analyse Crystal structure of LIP5 N-terminal domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4TXP
Type: protein
Length: 456 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vacuolar protein sorting-associated protein VTA1 homolog
UniProt: Q9NP79
Pockets: 5 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 79% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vacuolar protein sorting-associated protein VTA1 homolog	protein	156	79% helix, 0% strand	Q9NP79
B	Vacuolar protein sorting-associated protein VTA1 homolog	protein	153	80% helix, 0% strand	Q9NP79
C	Vacuolar protein sorting-associated protein VTA1 homolog	protein	147	78% helix, 0% strand	Q9NP79

Pockets

5 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	971	0.77	0.80	82	empty
2	272	0.55	0.76	39	empty
3	164	0.50	0.78	27	empty
4	52	0.34	0.78	13	empty
5	74	0.29	0.73	19	empty

Interfaces

3 interfaces between chains.

B–C · 401 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 391 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 378 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

4TXP · Crystal structure of LIP5 N-terminal domain · the same entry in another collection · chain A against A, TM-score 1.00
Q9NP79 · AlphaFold monomer V2.0 prediction for vacuolar protein sorting- associated protein VTA1… · a predicted model of the same protein · chain C against A, TM-score 0.99

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 Q9NP79
Elsewhere: RCSB PDB 4TXP · PDBe 4TXP · UniProt Q9NP79

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