SMTL ID : 2vmc.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

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

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)(Non-functional Binders)

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)(Non-functional Binders)

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   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

Related Entries With Identical Sequence