SMTL ID : 4k1y.1

Crystal structure of Canavalia boliviana lectin in complex with Man1-3Man-OMe

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

4 x MMA- MAN: alpha-D-mannopyranose-(1-3)-methyl alpha-D-mannopyranoside(Non-covalent)

MMA-MAN.1: 9 residues within 4Å: Chain A: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.14, A:G.98, A:L.99, A:Y.100, A:R.228, A:Y.12, A:Y.12 Water bridges: A:R.228 MMA-MAN.2: 9 residues within 4Å: Chain B: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.14, B:G.98, B:L.99, B:Y.100, B:Y.100, B:R.228, B:Y.12 Water bridges: B:R.228, B:N.14, B:N.14 MMA-MAN.3: 9 residues within 4Å: Chain C: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.14, C:G.98, C:L.99, C:Y.100, C:Y.100, C:R.228, C:Y.12 Water bridges: C:R.228 MMA-MAN.4: 9 residues within 4Å: Chain D: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.14, D:G.98, D:L.99, D:Y.100, D:Y.100, D:R.228, D:Y.12

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

MN.5: 5 residues within 4Å: Chain A: E.8, D.10, D.19, H.24, S.34 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.8, A:D.10, A:D.19, A:H.24, H2O.1 MN.9: 4 residues within 4Å: Chain B: E.8, D.10, D.19, H.24 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.8, B:D.10, B:D.19, B:H.24, H2O.3 MN.13: 4 residues within 4Å: Chain C: E.8, D.10, D.19, H.24 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.8, C:D.10, C:D.19, C:H.24, H2O.4 MN.18: 4 residues within 4Å: Chain D: E.8, D.10, D.19, H.24 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.8, D:D.10, D:D.19, D:H.24, H2O.7

4 x CA: CALCIUM ION(Non-covalent)

CA.6: 4 residues within 4Å: Chain A: D.10, Y.12, N.14, D.19 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.10, A:D.10, A:Y.12, A:D.19, H2O.1 CA.10: 4 residues within 4Å: Chain B: D.10, Y.12, N.14, D.19 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.10, B:D.10, B:Y.12, B:D.19, H2O.2 CA.14: 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.4, H2O.6 CA.19: 4 residues within 4Å: Chain D: D.10, Y.12, N.14, D.19 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.10, D:D.10, D:Y.12, D:D.19, H2O.6

9 x CD: CADMIUM ION(Non-covalent)

CD.7: 3 residues within 4Å: Chain A: D.80, D.82, N.83 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.80, A:D.82, H2O.2, H2O.2 CD.8: 1 residues within 4Å: Chain A: D.235 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.235, A:D.235 CD.11: 2 residues within 4Å: Chain B: D.80, D.82 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.80, B:D.80, B:D.82, H2O.3, H2O.4 CD.12: 1 residues within 4Å: Chain B: D.235 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.235, B:D.235 CD.15: 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.80, C:D.82 CD.16: 2 residues within 4Å: Chain C: D.235, N.237 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.235, H2O.5 CD.17: 2 residues within 4Å: Chain C: E.87, E.183 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.87, C:E.183, H2O.6 CD.20: 3 residues within 4Å: Chain D: K.59, D.80, D.82 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.80, D:D.80, D:D.82, H2O.7, H2O.7 CD.21: 2 residues within 4Å: Chain D: D.235, N.237 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.235

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Bezerra, G.A. et al., Structural Studies of an Anti-Inflammatory Lectin from Canavalia boliviana Seeds in Complex with Dimannosides. Plos One (2014)

Release Date

2014-04-09

Peptides

Canavalia boliviana lectin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Canavalia boliviana lectin

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