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

Structure of the wild-type discoidin II from Dictyostelium discoideum

Coordinates

PDB Format Compare

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.1, H2O.1 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.5, H2O.5, H2O.6 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.10, H2O.10

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 B, 2 interactions with chain C, 1 interactions with chain A Metal complexes: B:D.68, B:D.68, C:D.68, C:D.68, A: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: 3 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:S.7, B:S.9, B:N.13, C:R.94, C:H.137

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
B

C
C

DISCOIDIN-2

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