SMTL ID : 3r52.1

Structure analysis of a wound-inducible lectin ipomoelin from sweet potato

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

4 x GYP: methyl alpha-D-glucopyranoside(Non-covalent)

GYP.1: 7 residues within 4Å: Chain A: G.26, G.27, Y.103, G.147, W.148, Y.149, D.151 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.27, A:G.147, A:W.148, A:Y.149, A:D.151 Water bridges: A:W.148 GYP.2: 7 residues within 4Å: Chain B: G.26, G.27, Y.103, G.147, W.148, Y.149, D.151 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.27, B:W.148, B:Y.149, B:Y.149 Water bridges: B:W.148 GYP.4: 6 residues within 4Å: Chain C: G.27, Y.103, G.147, W.148, Y.149, D.151 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.27, C:G.147, C:W.148, C:Y.149, C:Y.149 GYP.6: 7 residues within 4Å: Chain D: G.26, G.27, Y.103, G.147, W.148, Y.149, D.151 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:G.27, D:W.148, D:Y.149, D:Y.149 Water bridges: D:N.25

3 x CD: CADMIUM ION(Non-covalent)

CD.3: 2 residues within 4Å: Chain B: S.24, N.25 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:S.24, B:N.25, H2O.6, H2O.6, H2O.6 CD.5: 3 residues within 4Å: Chain C: S.24, N.25 Chain D: L.9 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:S.24, C:N.25, H2O.14, H2O.16, H2O.16 CD.7: 2 residues within 4Å: Chain D: S.24, N.25 6 PLIP interactions: 2 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:S.24, D:N.25, H2O.11, H2O.11, H2O.14, H2O.17

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chang, W.C. et al., Ipomoelin, a jacalin-related lectin with a compact tetrameric association and versatile carbohydrate binding properties regulated by its N terminus. Plos One (2012)

Release Date

2012-03-28

Peptides

Ipomoelin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Ipomoelin

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