SMTL ID : 2vme.1 (1 other biounit)

STRUCTURE OF THE WILD-TYPE DISCOIDIN II FROM DICTYOSTELIUM DISCOIDEUM

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-trimer

Ligands

3 x CA: CALCIUM ION(Non-covalent)

CA.1: 3 residues within 4Å: Chain A: N.39, S.40, D.47 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.40, A:D.47, H2O.23, H2O.24 CA.6: 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.128, H2O.129, H2O.132 CA.10: 3 residues within 4Å: Chain C: N.39, S.40, D.47 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:S.40, C:D.47, H2O.247, H2O.249

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 3 residues within 4Å: Chain A: D.68 Chain B: D.68 Chain C: D.68 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 2 interactions with chain B Metal complexes: C:D.68, C:D.68, A:D.68, B:D.68, B:D.68

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

CL.3: 3 residues within 4Å: Chain A: W.219 Chain B: W.219 Chain C: W.219 Ligand excluded by PLIP

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 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.19, A:R.94, A:H.137, C:A.12 GOL.5: 5 residues within 4Å: Chain A: D.209, Y.244 Chain B: Q.216, R.218, W.238 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.216, B:R.218 GOL.7: 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: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.19, B:R.94, B:H.137, A:A.12 GOL.8: 5 residues within 4Å: Chain B: D.209, Y.244 Chain C: Q.216, R.218, W.238 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:Q.216, C:R.218, B:D.209 GOL.9: 5 residues within 4Å: Chain B: Y.24, H.28, R.81, Q.86, H.144 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.28, B:R.81, B:R.81, B:Q.86, B:H.144 GOL.11: 5 residues within 4Å: Chain A: Q.216, R.218, W.238 Chain C: D.209, Y.244 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:D.209, A:Q.216, A:R.218 Water bridges: C:D.209 GOL.13: 4 residues within 4Å: Chain C: H.28, R.81, Q.86, H.144 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.81, C:R.81, C:Q.86, C:H.144

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.12: 14 residues within 4Å: Chain B: S.7, V.8, S.9, A.12, N.13 Chain C: R.19, F.62, V.64, R.94, N.99, V.100, W.102, A.135, H.137 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:R.94, C:H.137, B:S.7, B:S.9, B:N.13

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
B

C
C

DISCOIDIN-2

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