SMTL ID : 2dva.1

Crystal structure of peanut lectin GAL-BETA-1,3-GALNAC-ALPHA-O-ME (Methyl-T-antigen) complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

4 x MGC- GAL: beta-D-galactopyranose-(1-3)-methyl 2-acetamido-2-deoxy-alpha-D-galactopyranoside(Non-covalent)

MGC-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 5 PLIP interactions: 5 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:S.211, A:L.212, A:G.213, A:G.214 Water bridges: A:G.102, A:E.129, A:N.41 MGC-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 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.80, 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:Y.125, B:E.129, B:N.41, B:N.41 MGC-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 4 PLIP interactions: 4 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 Water bridges: C:Y.125, C:Y.125, C:N.41 MGC-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 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.80, D:D.83, D:N.127, D:S.211, D:S.211, D:L.212, D:G.213, D:G.214 Water bridges: D:G.102, D:G.104, D:N.41

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

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.6, H2O.6 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.17, H2O.17 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.25, H2O.30 CA.13: 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.33, H2O.33

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

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.6, H2O.6 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.17, H2O.17 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.14: 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.33, H2O.33

2 x SO4: SULFATE ION(Non-covalent)

SO4.9: 6 residues within 4Å: Chain A: E.13 Chain B: R.53, S.56, A.58, T.59, T.231 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.56, B:S.56 Water bridges: B:R.53, B:A.58, B:T.59 Salt bridges: B:R.53 SO4.12: 5 residues within 4Å: Chain C: R.53, S.56, A.58, T.59, T.231 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:S.56, C:S.56 Water bridges: C:R.53, C:T.59, C:T.59 Salt bridges: C:R.53

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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