SMTL ID : 2vmd.1

Structure of the complex of discoidin II from Dictyostelium discoideum with beta-methyl-galactose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 5 residues within 4Å: Chain A: W.219 Chain B: W.219 Chain C: W.219 Ligands: CL.7, CL.13 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain A: W.219 Chain B: W.219 Chain C: W.219 Ligands: CL.1, CL.13 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain A: W.219 Chain B: W.219 Chain C: W.219 Ligands: CL.1, CL.7 Ligand excluded by PLIP

3 x CA: CALCIUM ION(Non-covalent)

CA.2: 3 residues within 4Å: Chain A: N.39, S.40, D.47 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.40, A:D.47, H2O.2, H2O.3, H2O.3 CA.8: 3 residues within 4Å: Chain B: N.39, S.40, D.47 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:S.40, B:D.47, H2O.11, H2O.12, H2O.12 CA.14: 3 residues within 4Å: Chain C: N.39, S.40, D.47 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:S.40, C:D.47, H2O.20, H2O.20, H2O.21

3 x MBG: methyl beta-D-galactopyranoside(Non-covalent)

MBG.3: 5 residues within 4Å: Chain A: Q.216, R.218, W.238 Chain B: D.209, Y.244 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.216, A:R.218, B:D.209 Water bridges: A:Q.216, A:Q.216, B:D.209 Salt bridges: A:R.218 MBG.9: 5 residues within 4Å: Chain B: Q.216, R.218, W.238 Chain C: D.209, Y.244 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:Q.216, B:R.218, C:D.209 Water bridges: B:Q.216, B:Q.216, C:D.209 Salt bridges: B:R.218 MBG.15: 5 residues within 4Å: Chain A: D.209, Y.244 Chain C: Q.216, R.218, W.238 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:Q.216, C:R.218, A:D.209 Water bridges: C:Q.216, C:Q.216, A:D.209 Salt bridges: C:R.218

6 x 1PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL(Non-covalent)

1PG.4: 7 residues within 4Å: Chain A: F.62, V.64, R.94, W.102, A.135, H.137 Chain B: A.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.94, A:H.137 Water bridges: A:R.19 1PG.5: 4 residues within 4Å: Chain A: K.59, K.92, H.137, Q.139 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.92, A:Q.139 1PG.10: 7 residues within 4Å: Chain B: F.62, V.64, R.94, W.102, A.135, H.137 Chain C: A.12 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.94, B:H.137 Water bridges: B:R.19 1PG.11: 4 residues within 4Å: Chain B: K.59, K.92, H.137, Q.139 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.92, B:Q.139 1PG.16: 7 residues within 4Å: Chain A: A.12 Chain C: F.62, V.64, R.94, W.102, A.135, H.137 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.94, C:H.137 Water bridges: C:R.19 1PG.17: 4 residues within 4Å: Chain C: K.59, K.92, H.137, Q.139 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.92, C:Q.139

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

EDO.6: 4 residues within 4Å: Chain A: Y.24, H.28, R.81, Q.86 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.28, A:R.81, A:Q.86 Water bridges: A:R.81 EDO.12: 4 residues within 4Å: Chain B: Y.24, H.28, R.81, Q.86 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.28, B:R.81, B:Q.86 Water bridges: B:R.81 EDO.18: 4 residues within 4Å: Chain C: Y.24, H.28, R.81, Q.86 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:H.28, C:R.81, C:Q.86 Water bridges: C:R.81

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Aragao, K.S. et al., Structure Determination of Discoidin II from Dictyostelium Discoideum and Carbohydrate Binding Properties of the Lectin Domain. Proteins (2008)

Release Date

2008-07-01

Peptides

DISCOIDIN-2: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

DISCOIDIN-2

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