SMTL ID : 3wcs.1

Crystal structure of plant lectin (ligand-bound form)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-tetramer

Ligands

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

MAN-NAG-GAL.1: 13 residues within 4Å: Chain A: G.103, G.104, L.105, L.128, Y.129, N.130, V.131, H.132, W.133, G.214, I.215, T.216, N.219 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.219, A:K.102, A:G.104, A:L.105, A:N.130, A:N.130, A:V.131, A:I.215, A:T.216, A:T.216 Water bridges: A:Y.129, A:D.86, A:D.86 Hydrophobic interactions: A:V.131 MAN-NAG-GAL.14: 13 residues within 4Å: Chain C: G.103, G.104, L.105, L.128, Y.129, N.130, V.131, H.132, W.133, G.214, I.215, T.216, N.219 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.219, C:K.102, C:G.104, C:L.105, C:N.130, C:N.130, C:V.131, C:I.215, C:T.216 Water bridges: C:Y.129, C:D.86, C:D.86 Hydrophobic interactions: C:V.131

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

MAN-NAG.2: 13 residues within 4Å: Chain B: D.86, 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.15: 13 residues within 4Å: Chain D: D.86, 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: 6 residues within 4Å: Chain A: N.12, E.13, 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:E.13, C:E.203 NAG.11: 5 residues within 4Å: Chain B: F.11, N.12, S.25 Chain D: E.203, W.204 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:N.12, D:E.203 NAG.16: 6 residues within 4Å: Chain A: E.203, W.204 Chain C: N.12, E.13, 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:E.13, A:E.203 NAG.24: 5 residues within 4Å: Chain B: E.203, W.204 Chain D: F.11, N.12, S.25 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:N.12, 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.12: 5 residues within 4Å: Chain B: E.124, D.126, D.134, H.139 Ligands: CA.13 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.5, H2O.5 MN.17: 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.6, H2O.6 MN.25: 5 residues within 4Å: Chain D: E.124, D.126, D.134, H.139 Ligands: CA.26 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.11, H2O.11

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:L.128, A:D.134, H2O.1, H2O.1 CA.13: 5 residues within 4Å: Chain B: D.126, L.128, N.130, D.134 Ligands: MN.12 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.126, B:L.128, B:D.134, H2O.5, H2O.5 CA.18: 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:L.128, C:D.134, H2O.6, H2O.6 CA.26: 5 residues within 4Å: Chain D: D.126, L.128, N.130, D.134 Ligands: MN.25 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.126, D:L.128, D:D.134, H2O.11, H2O.11

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

EDO.6: 5 residues within 4Å: Chain A: L.166, S.179, V.181 Chain B: T.168, V.177 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.168, B:T.168, A:S.179 EDO.7: 4 residues within 4Å: Chain A: T.168, V.177 Chain B: L.166, S.179 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.179, A:T.168 EDO.8: 8 residues within 4Å: Chain A: S.2, Q.3, T.4, I.55, Q.56, S.232, K.233, L.234 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.3, A:T.4, A:Q.56, A:S.232 EDO.9: 7 residues within 4Å: Chain A: I.17, Q.19, V.95, G.96, S.97, Q.98, I.206 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.19, A:G.96, A:S.97 EDO.10: 8 residues within 4Å: Chain A: F.8, R.10, F.11, N.12, N.15, L.16 Chain C: S.2, W.204 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:N.12, A:N.15, C:S.2, C:S.2 EDO.19: 5 residues within 4Å: Chain C: L.166, S.179, V.181 Chain D: T.168, V.177 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.179, D:T.168 EDO.20: 4 residues within 4Å: Chain C: T.168, V.177 Chain D: L.166, S.179 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:T.168, C:T.168, D:S.179 EDO.21: 8 residues within 4Å: Chain C: S.2, Q.3, T.4, I.55, Q.56, S.232, K.233, L.234 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.3, C:Q.56, C:S.232 Water bridges: C:T.4, C:T.4 EDO.22: 7 residues within 4Å: Chain C: I.17, Q.19, V.95, G.96, S.97, Q.98, I.206 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.19, C:G.96, C:S.97 EDO.23: 8 residues within 4Å: Chain A: S.2, W.204 Chain C: F.8, R.10, F.11, N.12, N.15, L.16 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:N.12, C:N.15, A:S.2, A:S.2

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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