SMTL ID : 6dhb.1

Crystal structure of the human TIM-3 with bound Calcium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: I.92, G.94, N.97, D.98 Ligands: BEZ.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:I.92, A:G.94, A:D.98, H2O.4

1 x BEZ: BENZOIC ACID(Non-covalent)

BEZ.2: 9 residues within 4Å: Chain A: V.38, F.39, R.89, G.94, I.95, M.96, N.97, D.98 Ligands: CA.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.39, A:I.95 Hydrogen bonds: A:G.94, A:M.96, A:N.97, A:D.98 Water bridges: A:R.89 Salt bridges: A:R.89 pi-Stacking: A:F.39

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 7 residues within 4Å: Chain A: K.33, G.34, A.81, S.83, G.84, I.85, Y.86 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.34, A:A.81, A:I.85, A:I.85 EDO.4: 4 residues within 4Å: Chain A: V.53, W.56, W.61, L.62 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gandhi, A.K. et al., High resolution X-ray and NMR structural study of human T-cell immunoglobulin and mucin domain containing protein-3. Sci Rep (2018)

Release Date

2018-12-12

Peptides

Hepatitis A virus cellular receptor 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Hepatitis A virus cellular receptor 2