MolNFT v1 · #25188 · protein

Crystal structure of ribosomal protein S2P

1VI5 · 30S ribosomal protein S2P: “Crystal structure of ribosomal protein S2P”. X-ray diffraction, 3 pockets (best druggability 0.59). MolNFT v1 #25188 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1VI5
Type: protein
Length: 778 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 30S ribosomal protein S2P
UniProt: O29132
Pockets: 3 · best druggability 0.59

Structure

x-ray diffraction · 4 distinct chains · 38% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	30S ribosomal protein S2P	protein	198	36% helix, 15% strand	O29132
B	30S ribosomal protein S2P	protein	195	38% helix, 15% strand	O29132
C	30S ribosomal protein S2P	protein	193	39% helix, 16% strand	O29132
D	30S ribosomal protein S2P	protein	192	40% helix, 16% strand	O29132

Pockets

3 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	503	0.59	0.74	49	empty
2	222	0.48	0.74	30	empty
3	58	0.30	0.75	18	empty

Interfaces

4 interfaces between chains.

C–D · 731 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 659 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 455 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 264 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 modified (engineered).

Compared structures

1VI5 · Crystal structure of ribosomal protein S2P · the same entry in another collection · chain D against D, TM-score 1.00
O29132 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S2 (O29132) · 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 O29132
Elsewhere: RCSB PDB 1VI5 · PDBe 1VI5 · UniProt O29132

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