SMTL ID : 4k1z.1

Crystal structure of Canavalia boliviana lectin in complex with Man1-4Man-OMe

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

4 x MMA- MAN: alpha-D-mannopyranose-(1-4)-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:Y.100, A:R.228, A:Y.12, A:Y.12 Water bridges: A:G.98, A:T.226, 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 1 PLIP interactions: 1 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 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 2 PLIP interactions: 2 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, 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 Water bridges: D:R.228

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

MN.5: 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.1, H2O.1 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.6, H2O.7 MN.17: 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.11, H2O.12 MN.20: 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.16, H2O.16

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: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.10, A:D.10, A:D.19, H2O.1, H2O.1 CA.12: 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.6, H2O.6 CA.18: 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.11, H2O.12 CA.21: 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.16, H2O.17

9 x CD: CADMIUM ION(Non-covalent)

CD.7: 1 residues within 4Å: Chain A: K.30 No protein-ligand interaction detected (PLIP) CD.8: 5 residues within 4Å: Chain A: L.107, N.131, G.152, N.153 Chain B: E.122 No protein-ligand interaction detected (PLIP) CD.9: 2 residues within 4Å: Chain A: D.80, D.82 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.80, H2O.3, H2O.3, H2O.4, H2O.4 CD.10: 2 residues within 4Å: Chain A: D.82, W.182 No protein-ligand interaction detected (PLIP) CD.13: 4 residues within 4Å: Chain B: L.107, N.131, G.152, N.153 No protein-ligand interaction detected (PLIP) CD.14: 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.82, B:D.82, H2O.8, H2O.10 CD.19: 4 residues within 4Å: Chain C: L.107, N.131, G.152, N.153 No protein-ligand interaction detected (PLIP) CD.22: 5 residues within 4Å: Chain C: E.122 Chain D: L.107, N.131, G.152, N.153 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:N.131 CD.23: 2 residues within 4Å: Chain D: D.80, D.82 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.80, D:D.82, H2O.20, H2O.20, H2O.21

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.15: 2 residues within 4Å: Chain B: D.80, N.83 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain B: N.55, R.60 Chain D: N.55, G.58 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   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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