SMTL ID : 5v6i.1

Glycan binding protein Y3 from mushroom Coprinus comatus possesses anti-leukemic activity - Pt derivative

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x NHE: 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID(Non-covalent)

NHE.1: 8 residues within 4Å: Chain A: I.65, A.67, S.68, N.71, I.91, A.95, P.96, F.97 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.65 Hydrogen bonds: A:S.68, A:N.71, A:F.97 NHE.18: 9 residues within 4Å: Chain B: R.66, A.67, S.68, N.71, I.91, A.95, P.96, F.97, F.99 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:R.66 Hydrogen bonds: B:S.68, B:N.71, B:F.97

4 x PT: PLATINUM (II) ION(Non-covalent)(Non-functional Binders)

PT.2: 5 residues within 4Å: Chain B: R.82 Ligands: CL.10, CL.11, CL.12, CL.13 No protein-ligand interaction detected (PLIP) PT.3: 2 residues within 4Å: Chain B: C.6, C.83 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.6 PT.4: 4 residues within 4Å: Ligands: CL.6, CL.7, CL.8, CL.9 No protein-ligand interaction detected (PLIP) PT.5: 4 residues within 4Å: Chain B: R.37 Ligands: CL.15, CL.16, CL.17 No protein-ligand interaction detected (PLIP)

12 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 5 residues within 4Å: Chain B: R.88, L.98 Ligands: PT.4, CL.9, CL.15 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain B: S.5 Ligands: PT.4, CL.8, CL.9 Ligand excluded by PLIP CL.8: 6 residues within 4Å: Chain B: P.3, S.5, R.88, G.89 Ligands: PT.4, CL.7 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Ligands: PT.4, CL.6, CL.7 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain B: Q.1, R.82 Ligands: PT.2, CL.12, CL.13 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Ligands: PT.2, CL.12, CL.13 Ligand excluded by PLIP CL.12: 6 residues within 4Å: Chain B: A.78, N.81, R.82 Ligands: PT.2, CL.10, CL.11 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Ligands: PT.2, CL.10, CL.11 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain B: S.5, C.6 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Ligands: PT.5, CL.6, CL.16 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain A: S.109 Chain B: R.37 Ligands: PT.5, CL.15, CL.17 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain B: R.37 Ligands: PT.5, CL.16 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, P. et al., Cytotoxic protein from the mushroom Coprinus comatus possesses a unique mode for glycan binding and specificity. Proc. Natl. Acad. Sci. U.S.A. (2017)

Release Date

2017-08-16

Peptides

TMV resistance protein Y3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

TMV resistance protein Y3