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Crystal structure of a human P14.5, a translational inhibitor reveals different mode of ligand binding near the invariant residues of the YJGF/UK114 protein family

Analyse Crystal structure of a human P14.5, a translational inhibitor reveals different… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1ONI
Type: protein
Length: 1,210 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 14.5 kda translational inhibitor protein
UniProt: P52758
Ligands: BEZ
Pockets: 18 · best druggability 0.83

Structure

x-ray diffraction · 3 distinct chains · 27% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	14.5 kda translational inhibitor protein	protein	136	28% helix, 33% strand	P52758
B, C, D, E, F, G	14.5 kda translational inhibitor protein	protein	134	28% helix, 35% strand	P52758
H, I	14.5 kda translational inhibitor protein	protein	135	26% helix, 33% strand	P52758

Ligands and binding sites

BEZ · Benzoic acid · ligand · 13 copies · chains A, B, C, D, F, E, G, H, I

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

Pockets

18 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	170	0.83	0.99	27	empty
2	168	0.83	0.98	27	empty
3	162	0.82	0.98	25	empty
4	552	0.74	0.82	64	empty
5	157	0.74	0.92	28	BEZ

Interfaces

17 interfaces between chains.

H–I · 1243 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1235 Å² buried · 19 hydrogen bonds · protein-protein
D–E · 1220 Å² buried · 21 hydrogen bonds · protein-protein
B–C · 1219 Å² buried · 19 hydrogen bonds · protein-protein
G–H · 1217 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

1ONI · Crystal structure of a human p14.5, a translational inhibitor reveals different mode of… · the same entry in another collection · chain H against H, TM-score 1.00
P52758 · AlphaFold monomer V2.0 prediction for 2-IMINOBUTANOATE/2-iminopropanoate deaminase… · a predicted model of the same protein · chain H against A, TM-score 0.98

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 P52758
Elsewhere: RCSB PDB 1ONI · PDBe 1ONI · UniProt P52758

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