MolNFT v1 · #128401 · protein

Beta domain of human transcobalamin bound to cyanocobalamin

5NP4 · Transcobalamin-2: “Beta domain of human transcobalamin bound to cyanocobalamin”. X-ray diffraction, 1 ligand (CNC), 1 pocket (best druggability 0.27). MolNFT v1 #128401 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5NP4
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: CNC
Pockets: 1 · best druggability 0.27

Structure

x-ray diffraction · 1 distinct chain · 9% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Transcobalamin-2	protein	106	9% helix, 45% strand	P20062

Ligands and binding sites

CNC · Cyanocobalamin · ligand · chains A
GOL · Glycerol · additive · 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	53	0.27	0.74	14	empty

Compared structures

5NP4 · Beta domain of human transcobalamin bound to cyanocobalamin · 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 0.95

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 5NP4 · PDBe 5NP4 · UniProt P20062

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