SMTL ID : 2wn2.1

Structure of the discoidin I from Dictyostelium discoideum in complex with galactose beta 1-3 galNAc at 1.8 A resolution.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

homo-trimer

Ligands

3 x NGA- GAL: beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose(Non-covalent)(Non-functional Binders)

NGA-GAL.1: 11 residues within 4Å: Chain A: Y.167, D.170, Q.205, D.207, Y.242, S.243 Chain B: Q.214, R.216, W.236, N.237 Ligands: A2G.4 12 PLIP interactions: 6 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:Y.167, A:D.207, A:S.243, A:S.243, B:R.216, B:W.236, B:N.237, B:N.237 Water bridges: A:Q.205, A:Q.205, B:Q.214 Salt bridges: B:R.216 NGA-GAL.2: 11 residues within 4Å: Chain B: Y.167, D.170, Q.205, D.207, Y.242, S.243 Chain C: Q.214, R.216, W.236, N.237 Ligands: A2G.10 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain C Hydrogen bonds: B:S.243, B:S.243, C:R.216, C:W.236, C:N.237, C:N.237 Water bridges: B:Q.205, B:Y.242, C:Q.214 Salt bridges: C:R.216 NGA-GAL.3: 11 residues within 4Å: Chain A: Q.214, R.216, W.236, N.237 Chain C: Y.167, D.170, Q.205, D.207, Y.242, S.243 Ligands: A2G.15 11 PLIP interactions: 5 interactions with chain C, 6 interactions with chain A Hydrogen bonds: C:D.207, C:S.243, C:S.243, A:R.216, A:W.236, A:N.237, A:N.237 Water bridges: C:Q.205, C:Q.205, A:Q.214 Salt bridges: A:R.216

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

A2G.4: 8 residues within 4Å: Chain A: D.207, Y.242 Chain B: Q.214, R.216, W.236, N.237 Ligands: NGA-GAL.1, NGA-GAL.1 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.214, B:R.216, B:W.236, B:N.237, B:N.237 Salt bridges: B:R.216 A2G.10: 8 residues within 4Å: Chain B: D.207, Y.242 Chain C: Q.214, R.216, W.236, N.237 Ligands: NGA-GAL.2, NGA-GAL.2 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.216, C:W.236, C:N.237, C:N.237 Water bridges: C:Q.214 Salt bridges: C:R.216 A2G.15: 8 residues within 4Å: Chain A: Q.214, R.216, W.236, N.237 Chain C: D.207, Y.242 Ligands: NGA-GAL.3, NGA-GAL.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.216, A:W.236, A:N.237, A:N.237 Water bridges: A:Q.214 Salt bridges: A:R.216

3 x CA: CALCIUM ION(Non-functional Binders)

CA.5: 4 residues within 4Å: Chain A: D.165, D.204, D.247 Chain B: Q.220 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.204, A:D.247, A:D.247, H2O.27, H2O.27 CA.11: 4 residues within 4Å: Chain B: D.165, D.204, D.247 Chain C: Q.220 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.204, B:D.247, B:D.247, H2O.40, H2O.40 CA.16: 4 residues within 4Å: Chain A: Q.220 Chain C: D.165, D.204, D.247 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.165, C:D.204, C:D.247, C:D.247, H2O.13

1 x SO4: SULFATE ION(Non-covalent)

SO4.6: 9 residues within 4Å: Chain A: S.158, V.159, T.160 Chain B: S.158, V.159, T.160 Chain C: S.158, V.159, T.160 9 PLIP interactions: 4 interactions with chain B, 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: B:S.158, B:T.160, B:T.160, C:T.160, C:T.160, A:S.158 Water bridges: B:S.158, C:S.158, A:S.158

8 x GOL: GLYCEROL(Non-covalent)(Non-functional Binders)

GOL.7: 4 residues within 4Å: Chain A: R.105, V.110, T.111, H.122 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.105, A:R.105, A:T.111, A:T.111 GOL.8: 6 residues within 4Å: Chain A: Y.24, H.28, C.52, R.80, Q.85, H.143 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.28, A:R.80, A:Q.85, A:Q.85 Water bridges: A:Y.24, A:Y.24, A:R.80 GOL.12: 4 residues within 4Å: Chain B: R.105, V.110, T.111, H.122 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.105, B:T.111, B:T.111, B:T.111, B:H.122 Water bridges: B:T.111 GOL.13: 6 residues within 4Å: Chain B: Y.24, H.28, C.52, R.80, Q.85, H.143 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.28, B:R.80, B:Q.85 Water bridges: B:R.80, B:R.80 GOL.14: 7 residues within 4Å: Chain A: A.12 Chain B: R.19, V.63, R.93, W.101, A.134, H.136 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.19, B:H.136, A:A.12 GOL.17: 3 residues within 4Å: Chain C: R.105, T.111, H.122 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.105, C:R.105, C:T.111, C:H.122 Water bridges: C:T.111 GOL.18: 6 residues within 4Å: Chain C: Y.24, H.28, C.52, R.80, Q.85, H.143 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.80, C:Q.85 Water bridges: C:R.80, C:R.80 GOL.19: 7 residues within 4Å: Chain B: A.12 Chain C: R.19, Y.61, R.93, W.101, A.134, H.136 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:A.12, C:R.19, C:R.93 Water bridges: C:R.19, C:R.19

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

1PG.9: 11 residues within 4Å: Chain A: R.19, T.58, Y.61, V.63, K.91, R.93, W.101, H.136 Chain C: Q.9, A.12, N.13 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.19, A:T.58, A:K.91, A:R.93 Water bridges: A:R.19, A:R.93

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Mathieu, S. et al., Discoidin I from Dictyostelium Discoideum and Interactions with Oligosaccharides: Specificity, Affinity, Crystal Structures and Comparison with Discoidin II. J.Mol.Biol. (2010)

Release Date

2010-05-26

Peptides

DISCOIDIN-1 SUBUNIT A: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

DISCOIDIN-1 SUBUNIT A

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