SMTL ID : 2vm9.1

Native structure of the recombinant discoidin II of Dictyostelium discoideum at 1.75 angstrom

Coordinates

PDB Format Compare

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.3, H2O.4, H2O.4 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.17, H2O.18, H2O.18 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.32, H2O.32, H2O.32

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   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
A

C
A

DISCOIDIN-2

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