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Crystal structure of folded and partially unfolded forms of aquifex aeolicus ribosomal protein L20

Analyse Crystal structure of folded and partially unfolded forms of aquifex aeolicus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2GHJ
Type: protein
Length: 386 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 50S ribosomal protein L20
UniProt: O67086
Ligands: SO4
Pockets: 5 · best druggability 0.67

Structure

x-ray diffraction · 2 distinct chains · 74% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	50S ribosomal protein L20	protein	101	73% helix, 0% strand	O67086
B, E	50S ribosomal protein L20	protein	92	74% helix, 0% strand	O67086

Ligands and binding sites

SO4 · Sulfate ion · ion · 6 copies · chains A, E, B, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	755	0.67	0.75	72	SO4
2	133	0.45	0.77	23	SO4
3	109	0.42	0.77	21	SO4
4	83	0.30	0.72	17	SO4
5	53	0.30	0.76	10	empty

Interfaces

6 interfaces between chains.

B–E · 1586 Å² buried · 14 hydrogen bonds · protein-protein
A–D · 1460 Å² buried · 15 hydrogen bonds · protein-protein
B–D · 575 Å² buried · 1 hydrogen bond · protein-protein
A–E · 571 Å² buried · 0 hydrogen bonds · protein-protein
A–B · 402 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 modified (engineered).

Compared structures

2GHJ · Crystal structure of folded and partially unfolded forms of Aquifex aeolicus ribosomal… · the same entry in another collection · chain A against A, TM-score 1.00
O67086 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L20 (O67086) · a predicted model of the same protein · chain A against A, TM-score 0.71

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 O67086
Elsewhere: RCSB PDB 2GHJ · PDBe 2GHJ · UniProt O67086

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