SMTL ID : 2wn3.1

Crystal structure of Discoidin I from Dictyostelium discoideum in complex with the disaccharide GalNAc beta 1-3 galactose, at 1.6 A resolution.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

homo-trimer

Ligands

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

GAL-NGA.1: 6 residues within 4Å: Chain A: D.207, Y.242 Chain B: Q.214, R.216, W.236, N.237 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.216, B:N.237, B:N.237, A:D.207, B:Q.214, B:R.216, B:W.236, B:N.237 Water bridges: B:W.236, B:N.237, B:N.237 GAL-NGA.2: 6 residues within 4Å: Chain B: D.207, Y.242 Chain C: Q.214, R.216, W.236, N.237 10 PLIP interactions: 7 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:R.216, C:N.237, C:N.237, C:Q.214, C:R.216, C:W.236, C:N.237, B:D.207 Water bridges: C:R.216, C:W.236, C:N.237, C:N.237, B:Y.242, B:Y.242 GAL-NGA.3: 6 residues within 4Å: Chain A: Q.214, R.216, W.236, N.237 Chain C: D.207, Y.242 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:R.216, A:N.237, A:N.237, A:Q.214, A:R.216, A:W.236, A:N.237, C:D.207 Water bridges: A:W.236, A:N.237, A:N.237

3 x CA: CALCIUM ION(Non-covalent)

CA.4: 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.28, H2O.28 CA.8: 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.41, H2O.41 CA.11: 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.14

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 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 10 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C, 5 interactions with chain B Hydrogen bonds: A:T.160, C:T.160, C:T.160, B:S.158, B:S.158, B:T.160, B:T.160 Water bridges: A:S.158, C:S.158, B:S.158 SO4.6: 4 residues within 4Å: Chain B: R.105, V.110, T.111, H.122 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.111, B:T.111 Salt bridges: B:R.105, B:H.122 SO4.9: 1 residues within 4Å: Chain B: R.93 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.93 Salt bridges: B:R.93

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

1PG.7: 4 residues within 4Å: Chain A: K.91, E.103, N.106, G.107 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.91

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 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.12: 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: 4 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:R.19, C:R.93, C:H.136, B:A.12 Water bridges: C:R.19 GOL.13: 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

Links

RCSB   PDBe   PDBe-KB   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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