MolNFT v1 · #29728 · protein + RNA

The structure of a ribosomal protein L1 in complex with mRNA

1ZHO: “The structure of a ribosomal protein L1 in complex with mRNA”. X-ray diffraction, 1 ligand (K), 12 pockets (best druggability 0.78). MolNFT v1 #29728 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1ZHO
Type: protein + RNA
Length: 1,064 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MRNA; 50S ribosomal protein L1
UniProt: P27150
Ligands: K
Pockets: 12 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 33% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, D, F, H	MRNA	rna	38	—	—
A, C, E, G	50S ribosomal protein L1	protein	228	33% helix, 22% strand	P27150

Ligands and binding sites

K · Potassium ion · metal · 4 copies · chains D, C, H, G, B, A, F, E

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

Pockets

12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	621	0.78	0.84	45	empty
2	479	0.76	0.84	48	empty
3	1093	0.75	0.79	62	empty
4	905	0.75	0.79	60	empty
5	623	0.72	0.80	49	empty

Interfaces

12 interfaces between chains.

B–A · 1333 Å² buried · 26 hydrogen bonds · protein-nucleic
F–E · 1255 Å² buried · 28 hydrogen bonds · protein-nucleic
H–G · 1217 Å² buried · 24 hydrogen bonds · protein-nucleic
D–C · 1166 Å² buried · 23 hydrogen bonds · protein-nucleic
B–C · 774 Å² buried · 16 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 12 modified (engineered).

Compared structures

1ZHO · The structure of a ribosomal protein L1 in complex with mRNA · the same entry in another collection · chain G against G, TM-score 1.00
P27150 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L1 (P27150) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P27150
Elsewhere: RCSB PDB 1ZHO · PDBe 1ZHO · UniProt P27150

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