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Crystal structure of ribosomal protein TL5, one of the ctc family proteins, complexed with a fragment of 5S rRNA.

Analyse Crystal structure of ribosomal protein TL5, one of the ctc family proteins… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1FEU
Type: protein + RNA
Length: 454 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 19 nt fragment of 5S rRNA; 21 nt fragment of 5S rRNA; 50S ribosomal protein L25
UniProt: P56930
Ligands: MG, CD
Pockets: 6 · best druggability 0.69

Structure

x-ray diffraction · 4 distinct chains · 16% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, E	19 nt fragment of 5S rRNA	rna	19	—	—
C, F	21 nt fragment of 5S rRNA	rna	21	—	—
A	50S ribosomal protein L25	protein	185	15% helix, 44% strand	P56930
D	50S ribosomal protein L25	protein	189	18% helix, 43% strand	P56930

Ligands and binding sites

MG · Magnesium ion · metal · 17 copies · chains B, E, F, D, C, A
CD · Cadmium ion · metal · 13 copies · chains A, D

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

Pockets

6 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	758	0.69	0.77	47	empty
2	638	0.68	0.77	36	MG
3	212	0.50	0.77	20	MG
4	236	0.49	0.75	27	empty
5	150	0.47	0.78	14	MG

Interfaces

11 interfaces between chains.

E–F · 1005 Å² buried · 82 hydrogen bonds · nucleic-nucleic
B–C · 996 Å² buried · 89 hydrogen bonds · nucleic-nucleic
F–D · 535 Å² buried · 13 hydrogen bonds · protein-nucleic
C–A · 508 Å² buried · 19 hydrogen bonds · protein-nucleic
E–D · 455 Å² buried · 13 hydrogen bonds · protein-nucleic

Compared structures

1FEU · Crystal structure of ribosomal protein TL5, one of the ctc family proteins, complexed… · the same entry in another collection · chain D against D, TM-score 1.00
P56930 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L25 (P56930) · a predicted model of the same protein · chain D against A, TM-score 0.94

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 P56930
Elsewhere: RCSB PDB 1FEU · PDBe 1FEU · UniProt P56930

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