MolNFT v1 · #140034 · protein

Crystal structure of native ribt from bacillus subtilis

5XXS · Protein ribt: “Crystal structure of native ribt from bacillus subtilis”. X-ray diffraction, 2 ligands (COA, NA), 3 pockets (best druggability 0.44). MolNFT v1 #140034 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5XXS
Type: protein
Length: 240 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, NA
Pockets: 3 · best druggability 0.44

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein ribt (EC 2.3.1.-)	protein	117	40% helix, 30% strand	P17622
B	Protein ribt (EC 2.3.1.-)	protein	123	37% helix, 27% strand	P17622

Ligands and binding sites

COA · Coenzyme A · ligand · 2 copies · chains A, B
NA · Sodium ion · metal · chains A
GOL · Glycerol · additive · 4 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	142	0.44	0.76	23	COA
2	96	0.36	0.75	20	COA
3	91	0.32	0.73	18	empty

Interfaces

1 interface between chains.

A–B · 365 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5XXS · Crystal structure of native 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 A against A, TM-score 0.98

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 P17622
Elsewhere: RCSB PDB 5XXS · PDBe 5XXS · UniProt P17622

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