SMTL ID : 3ul2.1 (1 other biounit)

Galactose-specific lectin from Dolichos lablab in P6522 space group

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: D.148, F.150, N.152, D.156 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.148, A:F.150, A:D.156, H2O.1, H2O.1 CA.5: 4 residues within 4Å: Chain B: D.148, F.150, N.152, D.156 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.148, B:F.150, B:D.156, H2O.2, H2O.2 CA.9: 4 residues within 4Å: Chain C: D.148, F.150, N.152, D.156 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.148, C:F.150, C:D.156, H2O.4, H2O.4 CA.13: 4 residues within 4Å: Chain D: D.148, F.150, N.152, D.156 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.148, D:F.150, D:D.156, H2O.5, H2O.5

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

MN.2: 4 residues within 4Å: Chain A: E.146, D.148, D.156, H.161 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.146, A:D.148, A:D.156, A:H.161, H2O.1, H2O.1 MN.6: 4 residues within 4Å: Chain B: E.146, D.148, D.156, H.161 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.146, B:D.148, B:D.156, B:H.161, H2O.2, H2O.2 MN.10: 4 residues within 4Å: Chain C: E.146, D.148, D.156, H.161 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.146, C:D.148, C:D.156, C:H.161, H2O.3, H2O.4 MN.14: 4 residues within 4Å: Chain D: E.146, D.148, D.156, H.161 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.146, D:D.148, D:D.156, D:H.161, H2O.5, H2O.5

4 x GAL: beta-D-galactopyranose(Non-covalent)

GAL.3: 10 residues within 4Å: Chain A: A.107, D.108, G.125, G.126, F.150, N.152, G.236, L.237, S.238, Y.241 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.108, A:G.126, A:N.152, A:N.152, A:L.237 GAL.7: 10 residues within 4Å: Chain B: A.107, D.108, G.125, G.126, F.150, N.152, G.236, L.237, S.238, Y.241 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.108, B:G.126, B:N.152, B:N.152, B:L.237 GAL.11: 10 residues within 4Å: Chain C: A.107, D.108, G.125, G.126, F.150, N.152, G.236, L.237, S.238, Y.241 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.108, C:G.126, C:N.152, C:N.152, C:L.237 GAL.15: 10 residues within 4Å: Chain D: A.107, D.108, G.125, G.126, F.150, N.152, G.236, L.237, S.238, Y.241 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.108, D:G.126, D:N.152, D:L.237

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 4 residues within 4Å: Chain A: A.65, G.66, L.237, K.239 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.65, A:K.239 EDO.8: 3 residues within 4Å: Chain B: A.65, G.66, L.237 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.65, B:L.237 EDO.12: 4 residues within 4Å: Chain C: A.65, G.66, L.237, K.239 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.65, C:K.239 EDO.16: 3 residues within 4Å: Chain D: A.65, G.66, L.237 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:A.65, D:L.237

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Shetty, K.N. et al., Affinity of a galactose-specific legume lectin from Dolichos lablab to adenine revealed by X-ray cystallography. Iubmb Life (2013)

Release Date

2012-11-14

Peptides

Legume lectin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

C
B

D
D

Legume lectin

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