Research workbench

Joint X-ray and NMR refinement of yeast L30E-mRNA complex

Analyse Joint X-ray and NMR refinement of yeast L30E-mRNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1T0K
Type: protein + RNA
Length: 489 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-R(*GP*AP*CP*CP*GP*GP*AP*GP*UP*GP*UP*CP*C)-3'…
UniProt: P02928, P14120
Ligands: GLC
Pockets: 6 · best druggability 0.75

Structure

x-ray diffraction · 4 distinct chains · 45% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	5'-R(GPAPCPCPGPGPAPGPUPGPUPCP*C)-3'	rna	12	—	—
D	5'-R(GGPAPCPGPCPAPGPAPGPAPUPGPGPUPC)-3'	rna	15	—	—
A	Maltose-binding periplasmic protein	protein	365	45% helix, 19% strand	P02928
B	60S ribosomal protein L30	protein	97	42% helix, 15% strand	P14120

Ligands and binding sites

GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A

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

Pockets

6 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	439	0.75	0.84	37	GLC
2	170	0.51	0.79	34	empty
3	69	0.39	0.78	15	empty
4	91	0.35	0.74	17	empty
5	75	0.34	0.75	16	empty

Interfaces

4 interfaces between chains.

C–D · 794 Å² buried · 65 hydrogen bonds · nucleic-nucleic
D–B · 442 Å² buried · 11 hydrogen bonds · protein-nucleic
A–B · 233 Å² buried · 2 hydrogen bonds · protein-protein
C–B · 114 Å² buried · 2 hydrogen bonds · protein-nucleic

Compared structures

1T0K · Joint X-ray and NMR Refinement of Yeast L30e-mRNA complex · the same entry in another collection · chain C against C, TM-score 1.00
P14120 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L30 (P14120) · a predicted model of the same protein · chain B against A, TM-score 0.96

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 P02928
Every structure of UniProt P14120
Elsewhere: RCSB PDB 1T0K · PDBe 1T0K · UniProt P02928 · UniProt P14120

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