SMTL ID : 3wcr.1

Crystal structure of plant lectin (ligand-free form)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-tetramer

Ligands

4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 10 residues within 4Å: Chain A: R.10, F.11, N.12, V.24, S.25, G.28 Chain D: E.203, W.204 Ligands: BR.9, BR.36 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.24 Hydrogen bonds: A:R.10, A:N.12 NAG.11: 10 residues within 4Å: Chain B: R.10, F.11, N.12, T.14, V.24, S.25, G.28 Chain C: W.204 Ligands: BR.17, BR.29 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.24 Hydrogen bonds: B:R.10, B:N.12 NAG.22: 10 residues within 4Å: Chain B: E.203, W.204 Chain C: R.10, F.11, N.12, V.24, S.25, G.28 Ligands: BR.15, BR.30 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.24 Hydrogen bonds: C:R.10, C:N.12 NAG.32: 10 residues within 4Å: Chain A: W.204 Chain D: R.10, F.11, N.12, T.14, V.24, S.25, G.28 Ligands: BR.8, BR.38 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:V.24 Hydrogen bonds: D:R.10, D:N.12, D:T.14

38 x BR: BROMIDE ION(Non-covalent)

BR.2: 5 residues within 4Å: Chain A: S.71, F.72, S.227, W.228, S.229 Ligand excluded by PLIP BR.3: 3 residues within 4Å: Chain A: P.84, F.157, K.159 Ligand excluded by PLIP BR.4: 3 residues within 4Å: Chain A: P.41, D.77, P.79 Ligand excluded by PLIP BR.5: 3 residues within 4Å: Chain A: T.152, T.153, T.154 Ligand excluded by PLIP BR.6: 3 residues within 4Å: Chain A: G.103, G.104, I.215 Ligand excluded by PLIP BR.7: 4 residues within 4Å: Chain A: G.214, I.215, T.216, N.219 Ligand excluded by PLIP BR.8: 3 residues within 4Å: Chain A: E.203, W.204 Ligands: NAG.32 Ligand excluded by PLIP BR.9: 4 residues within 4Å: Chain A: N.12, E.13, V.24 Ligands: NAG.1 Ligand excluded by PLIP BR.10: 5 residues within 4Å: Chain A: T.4, Q.56, W.204 Chain D: F.8, N.15 Ligand excluded by PLIP BR.12: 1 residues within 4Å: Chain B: R.20 Ligand excluded by PLIP BR.13: 2 residues within 4Å: Chain B: Q.19, P.99 Ligand excluded by PLIP BR.14: 3 residues within 4Å: Chain B: S.97, Q.98, K.100 Ligand excluded by PLIP BR.15: 4 residues within 4Å: Chain B: P.202, E.203, W.204 Ligands: NAG.22 Ligand excluded by PLIP BR.16: 4 residues within 4Å: Chain B: G.214, I.215, T.216, N.219 Ligand excluded by PLIP BR.17: 4 residues within 4Å: Chain B: N.12, E.13, V.24 Ligands: NAG.11 Ligand excluded by PLIP BR.18: 3 residues within 4Å: Chain B: P.84, F.157, K.159 Ligand excluded by PLIP BR.19: 4 residues within 4Å: Chain B: S.71, S.227, W.228, S.229 Ligand excluded by PLIP BR.20: 2 residues within 4Å: Chain B: N.111, Y.112 Ligand excluded by PLIP BR.21: 4 residues within 4Å: Chain B: K.136, T.152, T.153, T.154 Ligand excluded by PLIP BR.23: 5 residues within 4Å: Chain C: S.71, F.72, S.227, W.228, S.229 Ligand excluded by PLIP BR.24: 3 residues within 4Å: Chain C: P.84, F.157, K.159 Ligand excluded by PLIP BR.25: 3 residues within 4Å: Chain C: P.41, D.77, P.79 Ligand excluded by PLIP BR.26: 3 residues within 4Å: Chain C: T.152, T.153, T.154 Ligand excluded by PLIP BR.27: 3 residues within 4Å: Chain C: G.103, G.104, I.215 Ligand excluded by PLIP BR.28: 4 residues within 4Å: Chain C: G.214, I.215, T.216, N.219 Ligand excluded by PLIP BR.29: 3 residues within 4Å: Chain C: E.203, W.204 Ligands: NAG.11 Ligand excluded by PLIP BR.30: 4 residues within 4Å: Chain C: N.12, E.13, V.24 Ligands: NAG.22 Ligand excluded by PLIP BR.31: 5 residues within 4Å: Chain B: F.8, N.15 Chain C: T.4, Q.56, W.204 Ligand excluded by PLIP BR.33: 1 residues within 4Å: Chain D: R.20 Ligand excluded by PLIP BR.34: 2 residues within 4Å: Chain D: Q.19, P.99 Ligand excluded by PLIP BR.35: 3 residues within 4Å: Chain D: S.97, Q.98, K.100 Ligand excluded by PLIP BR.36: 4 residues within 4Å: Chain D: P.202, E.203, W.204 Ligands: NAG.1 Ligand excluded by PLIP BR.37: 4 residues within 4Å: Chain D: G.214, I.215, T.216, N.219 Ligand excluded by PLIP BR.38: 4 residues within 4Å: Chain D: N.12, E.13, V.24 Ligands: NAG.32 Ligand excluded by PLIP BR.39: 3 residues within 4Å: Chain D: P.84, F.157, K.159 Ligand excluded by PLIP BR.40: 4 residues within 4Å: Chain D: S.71, S.227, W.228, S.229 Ligand excluded by PLIP BR.41: 2 residues within 4Å: Chain D: N.111, Y.112 Ligand excluded by PLIP BR.42: 4 residues within 4Å: Chain D: K.136, T.152, T.153, T.154 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Nagae, M. et al., Phytohemagglutinin from Phaseolus vulgaris (PHA-E) displays a novel glycan recognition mode using a common legume lectin fold. Glycobiology (2014)

Release Date

2014-04-09

Peptides

Erythroagglutinin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Erythroagglutinin

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