MolNFT v1 · #140970 · protein

Crystal structure of periplasmic vitamin B12 binding protein btuf of vibrio cholerae

5YSC · Vitamin B12-binding protein: “Crystal structure of periplasmic vitamin B12 binding protein btuf of vibrio cholerae”. X-ray diffraction, 2 ligands (CNC, SO4), 1 pocket (best druggability 0.56). MolNFT v1 #140970 on GenesisL1: 3D…

PDB: 5YSC
Type: protein
Length: 255 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vitamin B12-binding protein
UniProt: A5F5P5
Ligands: CNC, SO4
Pockets: 1 · best druggability 0.56

Structure

x-ray diffraction · 1 distinct chain · 44% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vitamin B12-binding protein	protein	255	44% helix, 14% strand	A5F5P5

Ligands and binding sites

CNC · Cyanocobalamin · ligand · chains A
SO4 · Sulfate ion · ion · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	292	0.56	0.76	38	CNC

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

5YSC · Crystal Structure of periplasmic Vitamin B12 binding protein BtuF of Vibrio cholerae · the same entry in another collection · chain A against A, TM-score 1.00
A5F5P5 · AlphaFold monomer V2.0 prediction for vitamin B12-binding protein (A5F5P5) · a predicted model of the same protein · chain A against A, TM-score 1.00

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 A5F5P5
Elsewhere: RCSB PDB 5YSC · PDBe 5YSC · UniProt A5F5P5

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