SMTL ID : 1n47.1

Isolectin B4 from Vicia villosa in complex with the Tn antigen

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-tetramer

Ligands

4 x NAG- FUC- NAG: alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-FUC-NAG.1: 5 residues within 4Å: Chain A: D.60, N.61, E.201 Chain B: P.13, N.14 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.14 NAG-FUC-NAG.2: 4 residues within 4Å: Chain A: P.13, N.14 Chain B: N.61, E.201 No protein-ligand interaction detected (PLIP) NAG-FUC-NAG.3: 4 residues within 4Å: Chain C: N.61, E.201 Chain D: P.13, N.14 No protein-ligand interaction detected (PLIP) NAG-FUC-NAG.4: 4 residues within 4Å: Chain C: P.13, N.14 Chain D: N.61, E.201 No protein-ligand interaction detected (PLIP)

4 x CA: CALCIUM ION(Non-covalent)

CA.5: 4 residues within 4Å: Chain A: D.125, Y.127, N.129, D.132 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.125, A:D.125, A:Y.127, A:D.132, H2O.1 CA.9: 4 residues within 4Å: Chain B: D.125, Y.127, N.129, D.132 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.125, B:Y.127, B:D.132, H2O.1, H2O.1 CA.13: 4 residues within 4Å: Chain C: D.125, Y.127, N.129, D.132 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.125, C:Y.127, C:D.132, H2O.1, H2O.2 CA.17: 5 residues within 4Å: Chain D: D.125, Y.127, N.129, D.132 Ligands: MN.18 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.125, D:D.125, D:Y.127, D:D.132, H2O.2

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

MN.6: 4 residues within 4Å: Chain A: E.123, D.125, D.132, H.137 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.123, A:D.125, A:D.132, A:H.137, H2O.1, H2O.1 MN.10: 4 residues within 4Å: Chain B: E.123, D.125, D.132, H.137 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.123, B:D.125, B:D.132, B:H.137, H2O.1, H2O.1 MN.14: 5 residues within 4Å: Chain C: E.123, D.125, D.132, H.137, S.147 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.123, C:D.125, C:D.132, C:H.137, H2O.1, H2O.2 MN.18: 5 residues within 4Å: Chain D: E.123, D.125, D.132, H.137 Ligands: CA.17 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.123, D:D.125, D:D.132, D:H.137, H2O.2

4 x SER: SERINE(Non-covalent)

SER.7: 3 residues within 4Å: Chain A: Y.127, N.129 Ligands: A2G.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.129 SER.11: 3 residues within 4Å: Chain B: Y.127, N.129 Ligands: A2G.12 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.129 SER.15: 2 residues within 4Å: Chain C: Y.127 Ligands: A2G.16 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.127 SER.19: 2 residues within 4Å: Chain D: Y.127 Ligands: A2G.20 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.129

4 x A2G: 2-acetamido-2-deoxy-alpha-D-galactopyranose(Non-covalent)

A2G.8: 10 residues within 4Å: Chain A: D.85, G.102, G.103, Y.127, N.129, G.212, L.213, N.214, V.217 Ligands: SER.7 7 PLIP interactions: 6 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:D.85, A:G.103, A:N.129, A:N.129, A:L.213, A:N.214, S.7 A2G.12: 10 residues within 4Å: Chain B: D.85, G.102, G.103, Y.127, N.129, G.212, L.213, N.214, V.217 Ligands: SER.11 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:D.85, B:G.103, B:N.129, B:N.129, B:L.213, S.11 A2G.16: 12 residues within 4Å: Chain C: A.84, D.85, G.102, G.103, F.104, Y.127, N.129, G.212, L.213, N.214, V.217 Ligands: SER.15 6 PLIP interactions: 5 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: C:F.104 Hydrogen bonds: C:D.85, C:G.103, C:N.129, C:L.213, S.15 A2G.20: 10 residues within 4Å: Chain D: D.85, G.102, G.103, Y.127, N.129, G.212, L.213, N.214, V.217 Ligands: SER.19 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.85, D:G.103, D:N.129, D:N.129, D:L.213

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Babino, A. et al., The crystal structure of a plant lectin in complex with the Tn antigen. FEBS Lett. (2003)

Release Date

2003-02-25

Peptides

Isolectin B4: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Isolectin B4