SMTL ID : 2dvb.1

Crystal structure of peanut lectin GAl-beta-1,6-GalNAc complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-tetramer

Ligands

1 x NGA- GAL: beta-D-galactopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-galactopyranose(Non-covalent)

NGA-GAL.1: 11 residues within 4Å: Chain A: D.80, A.82, D.83, G.103, G.104, Y.125, N.127, E.129, S.211, G.213, G.214 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.80, A:D.83, A:G.104, A:N.127, A:S.211, A:G.214 Water bridges: A:E.129

4 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.2: 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.5, H2O.5 CA.6: 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.15, H2O.15 CA.10: 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.26, H2O.26 CA.14: 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.35, H2O.35

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

MN.3: 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.5, H2O.5 MN.7: 5 residues within 4Å: Chain B: E.121, D.123, D.132, H.137, S.147 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.15, H2O.15 MN.11: 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.25, H2O.25 MN.15: 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.35, H2O.35

4 x SO4: SULFATE ION(Non-covalent)(Non-functional Binders)

SO4.4: 7 residues within 4Å: Chain A: R.53, S.56, A.58, T.59, T.231 Chain B: S.12, E.13 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.56, A:S.56 Salt bridges: A:R.53 Water bridges: B:E.13 SO4.8: 5 residues within 4Å: Chain B: R.53, S.56, A.58, T.59, T.231 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.56, B:S.56 Water bridges: B:R.53 Salt bridges: B:R.53 SO4.12: 5 residues within 4Å: Chain C: R.53, S.56, A.58, T.59, T.231 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.56, C:S.56 Water bridges: C:T.59, C:T.59 Salt bridges: C:R.53 SO4.16: 5 residues within 4Å: Chain D: R.53, S.56, A.58, T.59, T.231 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.56 Water bridges: D:S.57 Salt bridges: D:R.53

3 x GAL: beta-D-galactopyranose(Non-covalent)(Non-functional Binders)

GAL.5: 10 residues within 4Å: Chain B: D.80, A.82, D.83, G.103, G.104, Y.125, N.127, E.129, S.211, G.214 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:D.80, B:D.83, B:G.104, B:N.127, B:S.211, B:G.214 Water bridges: B:Y.125, B:E.129 GAL.9: 9 residues within 4Å: Chain C: D.80, D.83, G.103, G.104, Y.125, N.127, E.129, S.211, G.214 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:D.80, C:D.80, C:D.83, C:G.104, C:N.127, C:S.211, C:G.214 Water bridges: C:E.129, C:G.213 GAL.13: 9 residues within 4Å: Chain D: D.80, A.82, D.83, G.103, G.104, Y.125, N.127, S.211, G.214 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:D.80, D:D.83, D:G.104, D:N.127, D:S.211 Water bridges: D:E.129, D:L.212, D:G.214

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Natchiar, S.K. et al., Structural studies on peanut lectin complexed with disaccharides involving different linkages: further insights into the structure and interactions of the lectin. ACTA CRYSTALLOGR.,SECT.D (2006)

Release Date

2006-11-07

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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