SMTL ID : 2vm9.1

NATIVE STRUCTURE OF THE RECOMBINANT DISCOIDIN II OF DICTYOSTELIUM DISCOIDEUM AT 1.75 ANGSTROM

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 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 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.40, A:D.47, H2O.70, H2O.88, H2O.91 CA.10: 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.440, H2O.458, H2O.461 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.810, H2O.828, H2O.831

6 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.2: 7 residues within 4Å: Chain A: Y.24, H.28, S.53, R.81, Q.86, H.144 Ligands: PO4.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.24, A:Y.24, A:Y.24 Hydrogen bonds: A:R.81, A:Q.86 MPD.3: 3 residues within 4Å: Chain A: T.89, S.90, T.140 No protein-ligand interaction detected (PLIP) MPD.11: 7 residues within 4Å: Chain B: Y.24, H.28, S.53, R.81, Q.86, H.144 Ligands: PO4.15 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.24, B:Y.24, B:Y.24 Hydrogen bonds: B:R.81, B:Q.86 MPD.12: 3 residues within 4Å: Chain B: T.89, S.90, T.140 No protein-ligand interaction detected (PLIP) MPD.20: 7 residues within 4Å: Chain C: Y.24, H.28, S.53, R.81, Q.86, H.144 Ligands: PO4.24 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:Y.24, C:Y.24, C:Y.24 Hydrogen bonds: C:R.81, C:Q.86 MPD.21: 3 residues within 4Å: Chain C: T.89, S.90, T.140 No protein-ligand interaction detected (PLIP)

9 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 11 residues within 4Å: Chain A: V.208, M.217, W.219 Chain B: V.208, M.217, W.219 Chain C: V.208, M.217, W.219 Ligands: PO4.13, PO4.22 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.219 PO4.5: 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 Water bridges: A:S.7, A:S.77, A:N.124 PO4.6: 5 residues within 4Å: Chain A: H.28, F.46, R.81, H.84 Ligands: MPD.2 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:H.28, A:R.81, A:H.84 PO4.13: 11 residues within 4Å: Chain A: V.208, M.217, W.219 Chain B: V.208, M.217, W.219 Chain C: V.208, M.217, W.219 Ligands: PO4.4, PO4.22 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.219 PO4.14: 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 Water bridges: B:S.7, B:S.77, B:N.124 PO4.15: 5 residues within 4Å: Chain B: H.28, F.46, R.81, H.84 Ligands: MPD.11 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:H.28, B:R.81, B:H.84 PO4.22: 11 residues within 4Å: Chain A: V.208, M.217, W.219 Chain B: V.208, M.217, W.219 Chain C: V.208, M.217, W.219 Ligands: PO4.4, PO4.13 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:W.219 PO4.23: 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 Water bridges: C:S.7, C:S.77, C:N.124 PO4.24: 5 residues within 4Å: Chain C: H.28, F.46, R.81, H.84 Ligands: MPD.20 3 PLIP interactions: 3 interactions with chain C Salt bridges: C:H.28, C:R.81, C:H.84

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

CL.7: 4 residues within 4Å: Chain A: G.181, S.182, W.238, G.239 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: D.58, K.59, N.60 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: H.84, D.85, R.117 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain B: G.181, S.182, W.238, G.239 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain B: D.58, K.59, N.60 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain B: H.84, D.85, R.117 Ligand excluded by PLIP CL.25: 4 residues within 4Å: Chain C: G.181, S.182, W.238, G.239 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain C: D.58, K.59, N.60 Ligand excluded by PLIP CL.27: 3 residues within 4Å: Chain C: H.84, D.85, R.117 Ligand excluded by PLIP

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

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