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Crystal structure of ribosomal protein S2P

Analyse Crystal structure of ribosomal protein S2P in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1VI6
Type: protein
Length: 773 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 30S ribosomal protein S2P
UniProt: O29132
Ligands: NA
Pockets: 3 · best druggability 0.60

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	30S ribosomal protein S2P	protein	193	38% helix, 16% strand	O29132
C	30S ribosomal protein S2P	protein	194	38% helix, 15% strand	O29132

Ligands and binding sites

NA · Sodium ion · metal · 10 copies · chains A, B, C, D

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	220	0.60	0.81	26	empty
2	331	0.59	0.77	37	empty
3	59	0.33	0.76	13	empty

Interfaces

3 interfaces between chains.

A–B · 1151 Å² buried · 21 hydrogen bonds · protein-protein
C–D · 1144 Å² buried · 22 hydrogen bonds · protein-protein
A–D · 520 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

1VI6 · Crystal structure of ribosomal protein S2P · the same entry in another collection · chain A against A, TM-score 1.00
O29132 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S2 (O29132) · a predicted model of the same protein · chain A 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 O29132
Elsewhere: RCSB PDB 1VI6 · PDBe 1VI6 · UniProt O29132

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