SMTL ID : 3wog.1

Crystal structure plant lectin in complex with ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x MAN- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose(Non-covalent)

MAN-NAG.1: 12 residues within 4Å: Chain A: G.103, G.104, L.105, L.128, N.130, V.131, H.132, W.133, G.214, I.215, T.216, N.219 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.104, A:L.105, A:N.130, A:N.130, A:V.131, A:I.215, A:T.216, A:T.216, A:N.219 Hydrophobic interactions: A:V.131 MAN-NAG.2: 12 residues within 4Å: Chain B: G.103, G.104, L.105, L.128, N.130, V.131, H.132, W.133, G.214, I.215, T.216, N.219 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.86, B:G.104, B:L.105, B:N.130, B:N.130, B:I.215, B:T.216, B:T.216, B:N.219 Hydrophobic interactions: B:V.131 MAN-NAG.9: 12 residues within 4Å: Chain C: G.103, G.104, L.105, L.128, N.130, V.131, H.132, W.133, G.214, I.215, T.216, N.219 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:G.104, C:L.105, C:N.130, C:N.130, C:V.131, C:I.215, C:T.216, C:N.219 Hydrophobic interactions: C:V.131 MAN-NAG.10: 12 residues within 4Å: Chain D: G.103, G.104, L.105, L.128, N.130, V.131, H.132, W.133, G.214, I.215, T.216, N.219 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.86, D:G.104, D:L.105, D:N.130, D:N.130, D:I.215, D:T.216, D:N.219 Hydrophobic interactions: D:V.131

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

NAG.3: 7 residues within 4Å: Chain A: N.12, E.13, T.14, V.24, S.25 Chain C: E.203, W.204 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:V.24 Hydrogen bonds: A:N.12, A:E.13, A:T.14, C:E.203 NAG.6: 7 residues within 4Å: Chain B: F.11, N.12, E.13, V.24, S.25 Chain D: E.203, W.204 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain B Hydrogen bonds: D:E.203, B:N.12, B:T.14 Hydrophobic interactions: B:V.24 NAG.11: 7 residues within 4Å: Chain A: E.203, W.204 Chain C: N.12, E.13, T.14, V.24, S.25 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:V.24 Hydrogen bonds: C:N.12, C:E.13, C:T.14, A:E.203 NAG.14: 7 residues within 4Å: Chain B: E.203, W.204 Chain D: F.11, N.12, E.13, V.24, S.25 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:V.24 Hydrogen bonds: D:N.12, D:T.14, B:E.203

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.4: 4 residues within 4Å: Chain A: E.124, D.126, D.134, H.139 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.124, A:D.126, A:D.134, A:H.139, H2O.1, H2O.1 MN.7: 5 residues within 4Å: Chain B: E.124, D.126, D.134, H.139 Ligands: CA.8 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.124, B:D.126, B:D.134, B:H.139, H2O.2, H2O.2 MN.12: 4 residues within 4Å: Chain C: E.124, D.126, D.134, H.139 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.124, C:D.126, C:D.134, C:H.139, H2O.3, H2O.3 MN.15: 5 residues within 4Å: Chain D: E.124, D.126, D.134, H.139 Ligands: CA.16 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.124, D:D.126, D:D.134, D:H.139, H2O.4, H2O.4

4 x CA: CALCIUM ION(Non-covalent)

CA.5: 4 residues within 4Å: Chain A: D.126, L.128, N.130, D.134 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.126, A:D.126, A:L.128, H2O.1, H2O.1 CA.8: 5 residues within 4Å: Chain B: D.126, L.128, N.130, D.134 Ligands: MN.7 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.126, B:D.126, B:L.128, B:D.134, H2O.2 CA.13: 4 residues within 4Å: Chain C: D.126, L.128, N.130, D.134 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.126, C:D.126, C:L.128, H2O.3, H2O.3 CA.16: 5 residues within 4Å: Chain D: D.126, L.128, N.130, D.134 Ligands: MN.15 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.126, D:D.126, D:L.128, D:D.134, H2O.4

Links

RCSB   PDBe   PDBe-KB   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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