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MolNFT v1 · #97626 · protein

Crystal structure of haptocorrin in complex with cncbl

4KKI · Transcobalamin-1: “Crystal structure of haptocorrin in complex with cncbl”. X-ray diffraction, 3 ligands (CNC, NAG, CA), 4 pockets (best druggability 0.79). MolNFT v1 #97626 on GenesisL1: 3D structure, binding sites and pockets in…

PDB
4KKI
Type
protein
Length
398 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Transcobalamin-1
UniProt
P20061
Ligands
CNC, NAG, CA
Pockets
4 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 14% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ATranscobalamin-1protein39849% helix, 14% strandP20061

Ligands and binding sites

  • CNC · Cyanocobalamin · ligand · chains A
  • NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A
  • CA · Calcium ion · metal · chains A
  • PEG · Di(hydroxyethyl)ether · additive · 11 copies · chains A

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

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
111490.790.8179CNC, PEG
2580.390.8015PEG
3960.380.7515PEG
4780.350.7614PEG

Modifications

Observed in the structure: 7 glycan, 4 disulfide (N-glycosylation, disulfide).

Compared structures

  • 4KKI · Crystal Structure of Haptocorrin in Complex with CNCbl · the same entry in another collection · chain A against A, TM-score 1.00
  • P20061 · AlphaFold monomer V2.0 prediction for transcobalamin-1 (P20061) · a predicted model of the same protein · chain A against A, TM-score 0.97

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