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Crystal structure of selenomethionine labelled ribt from bacillus subtilis

Analyse Crystal structure of selenomethionine labelled ribt from bacillus subtilis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5XXR
Type: protein
Length: 236 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein ribt
EC: 2.3.1.-
UniProt: P17622
Ligands: COA
Pockets: 3 · best druggability 0.58

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein ribt (EC 2.3.1.-)	protein	123	39% helix, 28% strand	P17622
B	Protein ribt (EC 2.3.1.-)	protein	113	40% helix, 29% strand	P17622

Ligands and binding sites

COA · Coenzyme A · ligand · 2 copies · chains A, B

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

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	328	0.58	0.77	35	COA
2	129	0.43	0.76	21	COA
3	125	0.37	0.73	23	empty

Interfaces

1 interface between chains.

A–B · 340 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 10 modified (engineered).

Compared structures

5XXR · Crystal structure of selenomethionine labelled RIBT from Bacillus subtilis · the same entry in another collection · chain A against A, TM-score 1.00
P17622 · AlphaFold monomer V2.0 prediction for protein ribt (P17622) · a predicted model of the same protein · chain B against A, TM-score 0.98

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P17622
Elsewhere: RCSB PDB 5XXR · PDBe 5XXR · UniProt P17622

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