SMTL ID : 1v6i.1

Peanut lectin-lactose complex in acidic pH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-tetramer

Ligands

4 x GLC- GAL: beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose(Non-covalent)

GLC-GAL.1: 11 residues within 4Å: Chain A: D.80, A.82, D.83, G.103, G.104, Y.125, N.127, S.211, L.212, G.213, G.214 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.80, A:D.83, A:G.104, A:N.127, A:S.211, A:S.211, A:L.212, A:G.213, A:G.214 Water bridges: A:G.213 GLC-GAL.2: 11 residues within 4Å: Chain B: D.80, A.82, D.83, G.103, G.104, Y.125, N.127, S.211, L.212, G.213, G.214 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.80, B:D.83, B:G.104, B:N.127, B:S.211, B:S.211, B:L.212, B:G.213, B:G.214 Water bridges: B:E.129, B:E.129 GLC-GAL.3: 11 residues within 4Å: Chain C: D.80, A.82, D.83, G.103, G.104, Y.125, N.127, S.211, L.212, G.213, G.214 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:D.80, C:D.83, C:G.104, C:N.127, C:S.211, C:S.211, C:L.212, C:G.213, C:G.214 Water bridges: C:Y.125, C:Y.125 GLC-GAL.4: 11 residues within 4Å: Chain D: D.80, A.82, D.83, G.103, G.104, Y.125, N.127, S.211, L.212, G.213, G.214 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.80, D:D.83, D:G.104, D:N.127, D:S.211, D:S.211, D:L.212, D:G.213, D:G.214 Water bridges: D:G.102, D:E.129

4 x CA: CALCIUM ION(Non-covalent)

CA.5: 4 residues within 4Å: Chain A: D.123, Y.125, N.127, D.132 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.123, A:Y.125, A:D.132, H2O.1, H2O.1 CA.7: 4 residues within 4Å: Chain B: D.123, Y.125, N.127, D.132 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.123, B:Y.125, B:D.132, H2O.5, H2O.5 CA.9: 4 residues within 4Å: Chain C: D.123, Y.125, N.127, D.132 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.123, C:Y.125, C:D.132, H2O.10, H2O.10 CA.11: 4 residues within 4Å: Chain D: D.123, Y.125, N.127, D.132 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.123, D:Y.125, D:D.132, H2O.13, H2O.14

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

MN.6: 4 residues within 4Å: Chain A: E.121, D.123, D.132, H.137 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.121, A:D.123, A:D.132, A:H.137, H2O.1, H2O.1 MN.8: 4 residues within 4Å: Chain B: E.121, D.123, D.132, H.137 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.121, B:D.123, B:D.132, B:H.137, H2O.5, H2O.5 MN.10: 4 residues within 4Å: Chain C: E.121, D.123, D.132, H.137 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.121, C:D.123, C:D.132, C:H.137, H2O.10, H2O.10 MN.12: 4 residues within 4Å: Chain D: E.121, D.123, D.132, H.137 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.121, D:D.123, D:D.132, D:H.137, H2O.14, H2O.14

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kundhavai Natchiar, S. et al., Structural plasticity of peanut lectin: an X-ray analysis involving variation in pH, ligand binding and crystal structure. Acta Crystallogr.,Sect.D (2004)

Release Date

2004-02-10

Peptides

Galactose-binding lectin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Galactose-binding lectin

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