SMTL ID : 4l8q.1

Crystal structure of Canavalia grandiflora seed lectin complexed with X-Man.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: D.10, Y.12, N.14, D.19 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.10, A:Y.12, A:D.19, H2O.1, H2O.1 CA.10: 4 residues within 4Å: Chain B: D.10, Y.12, N.14, D.19 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.10, B:Y.12, B:D.19, H2O.4, H2O.5 CA.19: 4 residues within 4Å: Chain C: D.10, Y.12, N.14, D.19 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.10, C:Y.12, C:D.19, H2O.8, H2O.8 CA.28: 4 residues within 4Å: Chain D: D.10, Y.12, N.14, D.19 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.10, D:Y.12, D:D.19, H2O.11, H2O.12

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

MN.2: 4 residues within 4Å: Chain A: E.8, D.10, D.19, H.24 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.8, A:D.10, A:D.19, A:H.24, H2O.3, H2O.3 MN.11: 4 residues within 4Å: Chain B: E.8, D.10, D.19, H.24 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.8, B:D.10, B:D.19, B:H.24, H2O.7, H2O.7 MN.20: 4 residues within 4Å: Chain C: E.8, D.10, D.19, H.24 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.8, C:D.10, C:D.19, C:H.24, H2O.10, H2O.10 MN.29: 4 residues within 4Å: Chain D: E.8, D.10, D.19, H.24 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.8, D:D.10, D:D.19, D:H.24, H2O.14, H2O.14

4 x XMM: 5-bromo-4-chloro-1H-indol-3-yl alpha-D-mannopyranoside(Non-covalent)

XMM.3: 9 residues within 4Å: Chain A: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.12, A:N.14, A:G.98, A:L.99, A:Y.100, A:Y.100, A:R.228 XMM.12: 9 residues within 4Å: Chain B: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.12, B:N.14, B:G.98, B:L.99, B:Y.100, B:Y.100, B:R.228 XMM.21: 9 residues within 4Å: Chain C: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Y.12, C:Y.12, C:G.98, C:L.99, C:Y.100, C:Y.100, C:R.228 XMM.30: 9 residues within 4Å: Chain D: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:Y.12, D:Y.12, D:G.98, D:L.99, D:Y.100, D:Y.100, D:R.228

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 4 residues within 4Å: Chain A: H.127, T.129 Chain D: A.125 Ligands: SO4.22 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:T.129 Salt bridges: A:H.127, D:K.114 SO4.13: 4 residues within 4Å: Chain B: H.127, T.129 Chain C: A.125 Ligands: SO4.31 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:T.129 Salt bridges: B:H.127, C:K.114 SO4.22: 4 residues within 4Å: Chain B: A.125 Chain C: H.127, T.129 Ligands: SO4.4 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Salt bridges: C:H.127, B:K.114 SO4.31: 4 residues within 4Å: Chain A: A.125 Chain D: H.127, T.129 Ligands: SO4.13 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Salt bridges: D:H.127, A:K.114

8 x CD: CADMIUM ION(Non-covalent)

CD.5: 2 residues within 4Å: Chain A: E.87, E.183 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.87, A:E.183, A:E.183, H2O.1, H2O.3 CD.6: 3 residues within 4Å: Chain A: K.59, D.80, D.82 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.80, A:D.82, A:D.82 CD.14: 2 residues within 4Å: Chain B: E.87, E.183 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.87, B:E.183, B:E.183, H2O.5, H2O.6 CD.15: 3 residues within 4Å: Chain B: K.59, D.80, D.82 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.80, B:D.82, B:D.82 CD.23: 2 residues within 4Å: Chain C: E.87, E.183 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.87, C:E.183, C:E.183, H2O.8, H2O.9 CD.24: 3 residues within 4Å: Chain C: K.59, D.80, D.82 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.80, C:D.82, C:D.82 CD.32: 2 residues within 4Å: Chain D: E.87, E.183 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.87, D:E.183, D:E.183, H2O.11, H2O.13 CD.33: 3 residues within 4Å: Chain D: K.59, D.80, D.82 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.80, D:D.82, D:D.82

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: S.56, D.82, W.182, E.183, A.186, A.189 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.56, A:S.56, A:W.182 GOL.8: 8 residues within 4Å: Chain A: I.52, I.53, D.192, A.193, T.194 Chain B: K.114, K.116, S.190 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.114, B:K.114, B:S.190, B:S.190, A:I.52 GOL.9: 4 residues within 4Å: Chain A: R.90, M.217, D.218 Chain D: Y.176 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.90 GOL.16: 6 residues within 4Å: Chain B: S.56, D.82, W.182, E.183, A.186, A.189 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.56, B:S.56, B:W.182 GOL.17: 8 residues within 4Å: Chain A: K.114, K.116, S.190 Chain B: I.52, I.53, D.192, A.193, T.194 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:I.52, A:K.114, A:K.114, A:S.190, A:S.190 GOL.18: 4 residues within 4Å: Chain B: R.90, M.217, D.218 Chain C: Y.176 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.90 GOL.25: 6 residues within 4Å: Chain C: S.56, D.82, W.182, E.183, A.186, A.189 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.56, C:S.56, C:W.182 GOL.26: 8 residues within 4Å: Chain C: I.52, I.53, D.192, A.193, T.194 Chain D: K.114, K.116, S.190 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:K.114, D:K.114, D:S.190, D:S.190, C:I.52, C:T.194 GOL.27: 4 residues within 4Å: Chain B: Y.176 Chain C: R.90, M.217, D.218 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.90 GOL.34: 6 residues within 4Å: Chain D: S.56, D.82, W.182, E.183, A.186, A.189 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.56, D:S.56, D:W.182 GOL.35: 8 residues within 4Å: Chain C: K.114, K.116, S.190 Chain D: I.52, I.53, D.192, A.193, T.194 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:K.114, C:K.114, C:S.190, C:S.190, D:I.52, D:T.194 GOL.36: 4 residues within 4Å: Chain A: Y.176 Chain D: R.90, M.217, D.218 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.90

Links

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Citation

Barroso-Neto, I.L. et al., Vasorelaxant activity of Canavalia grandiflora seed lectin: A structural analysis. Arch.Biochem.Biophys. (2014)

Release Date

2014-05-21

Peptides

Canavalia grandiflora seed lectin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Canavalia grandiflora seed lectin