SMTL ID : 2vmc.1

Structure of the complex of discoidin II from Dictyostelium discoideum with N-acetyl-galactosamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

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

CL.1: 5 residues within 4Å: Chain A: T.212 Chain B: T.212 Chain C: T.212 Ligands: CL.9, CL.17 Ligand excluded by PLIP CL.2: 5 residues within 4Å: Chain A: W.219 Chain B: W.219 Chain C: W.219 Ligands: CL.10, CL.18 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain A: T.212 Chain B: T.212 Chain C: T.212 Ligands: CL.1, CL.17 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain A: W.219 Chain B: W.219 Chain C: W.219 Ligands: CL.2, CL.18 Ligand excluded by PLIP CL.17: 5 residues within 4Å: Chain A: T.212 Chain B: T.212 Chain C: T.212 Ligands: CL.1, CL.9 Ligand excluded by PLIP CL.18: 5 residues within 4Å: Chain A: W.219 Chain B: W.219 Chain C: W.219 Ligands: CL.2, CL.10 Ligand excluded by PLIP

3 x CA: CALCIUM ION(Non-covalent)

CA.3: 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.4, H2O.4, H2O.4 CA.11: 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.17, H2O.18, H2O.18 CA.19: 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.31, H2O.32, H2O.32

3 x A2G: 2-acetamido-2-deoxy-alpha-D-galactopyranose(Non-covalent)

A2G.4: 6 residues within 4Å: Chain A: Q.216, R.218, W.238 Chain C: D.209, Y.244 Ligands: NGA.5 10 PLIP interactions: 4 interactions with chain C, 6 interactions with chain A Hydrogen bonds: C:D.209, A:Q.216, A:R.218 Water bridges: C:H.211, C:Y.244, C:Y.244, A:Q.216, A:Q.216, A:G.239 Salt bridges: A:R.218 A2G.12: 6 residues within 4Å: Chain A: D.209, Y.244 Chain B: Q.216, R.218, W.238 Ligands: NGA.13 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:Q.216, B:R.218, A:D.209 Water bridges: B:Q.216, B:Q.216, B:G.239, A:H.211, A:Y.244, A:Y.244 Salt bridges: B:R.218 A2G.20: 6 residues within 4Å: Chain B: D.209, Y.244 Chain C: Q.216, R.218, W.238 Ligands: NGA.21 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain C Hydrogen bonds: B:D.209, C:Q.216, C:R.218 Water bridges: B:H.211, B:Y.244, B:Y.244, C:Q.216, C:Q.216, C:G.239 Salt bridges: C:R.218

3 x NGA: 2-acetamido-2-deoxy-beta-D-galactopyranose(Non-covalent)

NGA.5: 6 residues within 4Å: Chain A: Q.216, R.218, W.238 Chain C: D.209, Y.244 Ligands: A2G.4 10 PLIP interactions: 4 interactions with chain C, 6 interactions with chain A Hydrogen bonds: C:D.209, A:Q.216, A:R.218 Water bridges: C:H.211, C:Y.244, C:Y.244, A:Q.216, A:Q.216, A:G.239 Salt bridges: A:R.218 NGA.13: 6 residues within 4Å: Chain A: D.209, Y.244 Chain B: Q.216, R.218, W.238 Ligands: A2G.12 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:Q.216, B:R.218, A:D.209 Water bridges: B:Q.216, B:Q.216, B:G.239, A:H.211, A:Y.244, A:Y.244 Salt bridges: B:R.218 NGA.21: 6 residues within 4Å: Chain B: D.209, Y.244 Chain C: Q.216, R.218, W.238 Ligands: A2G.20 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain C Hydrogen bonds: B:D.209, C:Q.216, C:R.218 Water bridges: B:H.211, B:Y.244, B:Y.244, C:Q.216, C:Q.216, C:G.239 Salt bridges: C:R.218

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

1PG.6: 7 residues within 4Å: Chain A: R.19, V.64, R.94, W.102, A.135, H.137 Chain C: A.12 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:R.94, A:H.137 Water bridges: A:R.19, C:N.13 1PG.7: 8 residues within 4Å: Chain A: Y.24, H.28, F.46, S.53, R.81, H.84, Q.86, H.144 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.81, A:Q.86 Water bridges: A:R.81, A:R.81 1PG.14: 7 residues within 4Å: Chain A: A.12 Chain B: R.19, V.64, R.94, W.102, A.135, H.137 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Water bridges: A:N.13, B:R.19 Hydrogen bonds: B:R.94, B:H.137 1PG.15: 8 residues within 4Å: Chain B: Y.24, H.28, F.46, S.53, R.81, H.84, Q.86, H.144 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.81, B:Q.86 Water bridges: B:R.81, B:R.81 1PG.22: 7 residues within 4Å: Chain B: A.12 Chain C: R.19, V.64, R.94, W.102, A.135, H.137 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:R.94, C:H.137 Water bridges: C:R.19, B:N.13 1PG.23: 8 residues within 4Å: Chain C: Y.24, H.28, F.46, S.53, R.81, H.84, Q.86, H.144 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.81, C:Q.86 Water bridges: C:R.81, C:R.81

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

EDO.8: 3 residues within 4Å: Chain A: S.7, T.122, Y.152 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.7, A:S.7 Water bridges: A:S.77, A:Y.152 EDO.16: 3 residues within 4Å: Chain B: S.7, T.122, Y.152 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.7, B:S.7 Water bridges: B:S.77, B:Y.152 EDO.24: 3 residues within 4Å: Chain C: S.7, T.122, Y.152 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.7, C:S.7 Water bridges: C:S.77, C:Y.152

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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