MolNFT v1 · #128506 · protein

Beta domain of human transcobalamin bound to co-beta-[2-(2,4- DIFLUOROPHENYL)ETHINYL]COBALAMIN

5NSA · Transcobalamin-2: “Beta domain of human transcobalamin bound to co-beta-[2-(2,4- DIFLUOROPHENYL)ETHINYL]COBALAMIN”. X-ray diffraction, 3 ligands (B12, 8FS, CA), 1 pocket (best druggability 0.31). MolNFT v1 #128506 on GenesisL1: 3D…

PDB: 5NSA
Type: protein
Length: 106 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transcobalamin-2
UniProt: P20062
Ligands: B12, 8FS, CA
Pockets: 1 · best druggability 0.31

Structure

x-ray diffraction · 1 distinct chain · 10% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Transcobalamin-2	protein	106	10% helix, 42% strand	P20062

Ligands and binding sites

B12 · Cobalamin · ligand · chains A
8FS · 1-ethynyl-2,4-difluorobenzene · ligand
CA · Calcium ion · metal · 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	51	0.31	0.77	11	empty

Compared structures

5NSA · Beta domain of human transcobalamin bound to Co-beta-[2-(2,4-difluorophenyl)ethinyl]cobala… · the same entry in another collection · chain A against A, TM-score 1.00
P20062 · AlphaFold monomer V2.0 prediction for transcobalamin-2 (P20062) · a predicted model of the same protein · chain A against A, TM-score 0.94

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 P20062
Elsewhere: RCSB PDB 5NSA · PDBe 5NSA · UniProt P20062

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