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Structure of protein L7AE bound to a K-turn derived from an archaeal box H/ACA srna

Analyse Structure of protein L7AE bound to a K-turn derived from an archaeal box H/ACA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1SDS
Type: protein + RNA
Length: 381 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Box H/ACA srna; 50S ribosomal protein L7AE
UniProt: P54066
Ligands: CA, K

Structure

x-ray diffraction · 4 distinct chains · 49% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D, E, F	Box H/ACA srna	rna	15	—	—
A	50S ribosomal protein L7AE	protein	115	49% helix, 17% strand	P54066
B	50S ribosomal protein L7AE	protein	109	49% helix, 17% strand	P54066
C	50S ribosomal protein L7AE	protein	112	49% helix, 17% strand	P54066

Ligands and binding sites

CA · Calcium ion · metal · 10 copies · chains D, E, F
K · Potassium ion · metal · chains E

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

Interfaces

6 interfaces between chains.

E–B · 449 Å² buried · 16 hydrogen bonds · protein-nucleic
F–C · 435 Å² buried · 15 hydrogen bonds · protein-nucleic
D–A · 431 Å² buried · 15 hydrogen bonds · protein-nucleic
F–A · 222 Å² buried · 11 hydrogen bonds · protein-nucleic
D–C · 220 Å² buried · 10 hydrogen bonds · protein-nucleic

Compared structures

1SDS · Structure of protein L7Ae bound to a K-turn derived from an archaeal box H/ACA sRNA · the same entry in another collection · chain C against C, TM-score 1.00
P54066 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L7AE (P54066) · 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 P54066
Elsewhere: RCSB PDB 1SDS · PDBe 1SDS · UniProt P54066

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