SMTL ID : 1y2x.1

Crystal structure of the tetragonal form of the common edible mushroom (Agaricus bisporus) lectin in complex with T-antigen and N-acetylglucosamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.36 Å

Oligo State

homo-tetramer

Ligands

4 x NGA- GAL: beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose(Non-covalent)

NGA-GAL.1: 10 residues within 4Å: Chain A: Y.27, A.28, S.47, G.48, H.71, N.72, Y.73, Y.97, R.106 Ligands: SER.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.28, A:S.47, A:G.48, A:N.72 Hydrophobic interactions: A:Y.73 Water bridges: A:R.106, A:R.106 NGA-GAL.2: 10 residues within 4Å: Chain B: Y.27, A.28, S.47, G.48, H.71, N.72, Y.73, Y.97, R.106 Ligands: SER.8 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.28, B:S.47, B:G.48, B:H.71, B:N.72, B:R.106 Hydrophobic interactions: B:Y.73 NGA-GAL.3: 10 residues within 4Å: Chain C: Y.27, A.28, S.47, G.48, H.71, N.72, Y.73, Y.97, R.106 Ligands: SER.10 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.28, C:S.47, C:G.48, C:N.72 NGA-GAL.4: 10 residues within 4Å: Chain D: Y.27, A.28, S.47, G.48, H.71, N.72, Y.73, Y.97, R.106 Ligands: SER.12 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:A.28, D:S.47, D:G.48, D:H.71, D:N.72 Water bridges: D:R.106, D:R.106

4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.5: 10 residues within 4Å: Chain A: D.78, I.79, V.80, T.81, N.82, I.101, R.102, Y.113, V.115, A.116 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:T.81, A:V.115 Hydrogen bonds: A:T.81, A:R.102, A:Y.113, A:Y.113 Salt bridges: A:R.102 NAG.7: 10 residues within 4Å: Chain B: D.78, I.79, V.80, T.81, N.82, I.101, R.102, Y.113, V.115, A.116 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:T.81, B:V.115 Hydrogen bonds: B:T.81, B:Y.96, B:R.102, B:Y.113 Salt bridges: B:R.102 NAG.9: 10 residues within 4Å: Chain C: D.78, I.79, V.80, T.81, N.82, I.101, R.102, Y.113, V.115, A.116 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:T.81, C:V.115 Hydrogen bonds: C:T.81, C:R.102, C:Y.113, C:Y.113 Salt bridges: C:R.102 NAG.11: 11 residues within 4Å: Chain D: D.78, I.79, V.80, T.81, N.82, I.101, R.102, A.105, Y.113, V.115, A.116 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:T.81, D:V.115 Hydrogen bonds: D:T.81, D:R.102, D:Y.113 Water bridges: D:Y.113, D:Y.113 Salt bridges: D:R.102

4 x SER: SERINE(Non-covalent)

SER.6: 2 residues within 4Å: Chain A: N.72 Ligands: NGA-GAL.1 No protein-ligand interaction detected (PLIP) SER.8: 2 residues within 4Å: Chain B: N.72 Ligands: NGA-GAL.2 No protein-ligand interaction detected (PLIP) SER.10: 2 residues within 4Å: Chain C: N.72 Ligands: NGA-GAL.3 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.72 SER.12: 2 residues within 4Å: Chain D: N.72 Ligands: NGA-GAL.4 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.72

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Carrizo, M.E. et al., The Antineoplastic Lectin of the Common Edible Mushroom (Agaricus bisporus) Has Two Binding Sites, Each Specific for a Different Configuration at a Single Epimeric Hydroxyl. J.Biol.Chem. (2005)

Release Date

2004-12-21

Peptides

lectin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

lectin

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