SMTL ID : 2vmd.1

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

Coordinates

PDB Format

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: 2 interactions with chain C, 5 interactions with chain B Hydrogen bonds: C:D.209, B:Q.216, B:R.218 Water bridges: C:D.209, B:Q.216, B:Q.216 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   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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