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Structure of the LARP1-unique domain DM15

Analyse Structure of the LARP1-unique domain DM15 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5C0V
Type: protein
Length: 572 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: La-related protein 1
UniProt: Q6PKG0
Ligands: SO4
Pockets: 8 · best druggability 0.61

Structure

x-ray diffraction · 4 distinct chains · 76% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	La-related protein 1	protein	148	74% helix, 0% strand	Q6PKG0
B	La-related protein 1	protein	142	77% helix, 0% strand	Q6PKG0
C	La-related protein 1	protein	145	75% helix, 0% strand	Q6PKG0
D	La-related protein 1	protein	137	77% helix, 0% strand	Q6PKG0

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains A, C, B, D

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

Pockets

8 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	320	0.61	0.78	48	SO4
2	295	0.58	0.77	43	SO4
3	333	0.54	0.74	41	empty
4	177	0.45	0.74	19	empty
5	89	0.43	0.79	16	empty

Interfaces

3 interfaces between chains.

A–C · 954 Å² buried · 9 hydrogen bonds · protein-protein
B–D · 717 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 360 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 modified (engineered).

Compared structures

5C0V · Structure of the LARP1-unique domain DM15 · the same entry in another collection · chain D against D, TM-score 1.00
Q6PKG0 · AlphaFold monomer V2.0 prediction for la-related protein 1 (Q6PKG0) · 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 Q6PKG0
Elsewhere: RCSB PDB 5C0V · PDBe 5C0V · UniProt Q6PKG0

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