MolNFT v1 · #8818 · protein + RNA

Crystal structure of a conserved ribosomal protein-RNA complex

1HC8 · Ribosomal protein L11: “Crystal structure of a conserved ribosomal protein-RNA complex”. X-ray diffraction, 3 ligands (MG, OS, K), 8 pockets (best druggability 0.69). MolNFT v1 #8818 on GenesisL1: 3D structure, binding sites and…

PDB: 1HC8
Type: protein + RNA
Length: 260 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribosomal protein L11; 58 nucleotide ribosomal 23S RNA domain
UniProt: P56210
Ligands: MG, OS, K
Pockets: 8 · best druggability 0.69

Structure

x-ray diffraction · 3 distinct chains · 50% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ribosomal protein L11	protein	74	50% helix, 8% strand	P56210
B	Ribosomal protein L11	protein	70	50% helix, 9% strand	P56210
C, D	58 nucleotide ribosomal 23S RNA domain	rna	58	—	—

Ligands and binding sites

MG · Magnesium ion · metal · 21 copies · chains C, D
OS · Osmium ion · metal · 4 copies · chains C, D
K · Potassium ion · metal · 2 copies · chains C, 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	886	0.69	0.76	55	MG, OS
2	288	0.66	0.83	23	MG, OS
3	318	0.65	0.82	23	MG, OS
4	99	0.35	0.75	15	MG
5	100	0.32	0.74	12	MG

Interfaces

5 interfaces between chains.

B–D · 1023 Å² buried · 31 hydrogen bonds · protein-nucleic
A–C · 1017 Å² buried · 31 hydrogen bonds · protein-nucleic
C–D · 77 Å² buried · 1 hydrogen bond · nucleic-nucleic
A–D · 72 Å² buried · 0 hydrogen bonds · protein-nucleic
B–C · 21 Å² buried · 0 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

1HC8 · Crystal structure of a conserved ribosomal protein-RNA complex · the same entry in another collection · chain A against A, TM-score 1.00
P56210 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L11 (P56210) · a predicted model of the same protein · chain B 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 P56210
Elsewhere: RCSB PDB 1HC8 · PDBe 1HC8 · UniProt P56210

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