- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.75 Å
- Oligo State
- homo-trimer
- Ligands
- 3 x NGA: 2-acetamido-2-deoxy-beta-D-galactopyranose(Non-covalent)
- 4 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)
MPD.2: 5 residues within 4Å:- Chain A: Y.24, H.28, R.80, Q.85, H.143
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:Y.24
- Hydrogen bonds: A:R.80, A:Q.85
- Water bridges: A:R.80
MPD.4: 6 residues within 4Å:- Chain A: R.19, V.63, R.93, W.101
- Chain C: A.12, N.13
6 PLIP interactions:1 interactions with chain C, 5 interactions with chain A- Hydrophobic interactions: C:A.12, A:V.63, A:W.101
- Hydrogen bonds: A:R.93, A:R.93
- Water bridges: A:R.19
MPD.9: 6 residues within 4Å:- Chain B: Y.24, H.28, R.80, Q.85, G.142, H.143
4 PLIP interactions:4 interactions with chain B- Hydrophobic interactions: B:Y.24
- Hydrogen bonds: B:R.80, B:Q.85
- Water bridges: B:R.80
MPD.17: 5 residues within 4Å:- Chain C: Y.24, H.28, R.80, Q.85, H.143
4 PLIP interactions:4 interactions with chain C- Hydrophobic interactions: C:Y.24
- Hydrogen bonds: C:R.80, C:Q.85
- Water bridges: C:R.80
- 7 x SO4: SULFATE ION(Non-functional Binders)
SO4.3: 4 residues within 4Å:- Chain A: R.105, V.110, T.111, H.122
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:T.111, A:T.111, A:T.111
- Salt bridges: A:R.105, A:H.122
SO4.5: 1 residues within 4Å:- Chain A: K.188
3 PLIP interactions:3 interactions with chain A- Water bridges: A:K.188, A:K.188
- Salt bridges: A:K.188
SO4.8: 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
8 PLIP interactions:3 interactions with chain C, 2 interactions with chain A, 3 interactions with chain B- Hydrogen bonds: C:T.160, C:T.160, A:S.158, B:S.158, B:T.160
- Water bridges: C:S.158, A:S.158, B:S.158
SO4.10: 4 residues within 4Å:- Chain B: R.105, V.110, T.111, H.122
7 PLIP interactions:7 interactions with chain B- Hydrogen bonds: B:T.111, B:T.111
- Water bridges: B:T.111, B:H.122, B:H.122
- Salt bridges: B:R.105, B:H.122
SO4.12: 3 residues within 4Å:- Chain B: D.115, R.116, N.117
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:D.115, B:R.116, B:N.117, B:N.117, B:T.118
SO4.18: 4 residues within 4Å:- Chain C: R.105, V.110, T.111, H.122
9 PLIP interactions:9 interactions with chain C- Hydrogen bonds: C:T.111, C:T.111
- Water bridges: C:T.111, C:T.111, C:H.122, C:H.122, C:H.122
- Salt bridges: C:R.105, C:H.122
SO4.20: 2 residues within 4Å:- Chain C: R.222, N.223
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:N.223
- Water bridges: C:R.222, C:R.222
- Salt bridges: C:R.222
- 3 x CA: CALCIUM ION(Non-covalent)
CA.6: 4 residues within 4Å:- Chain A: D.165, D.204, D.247
- Chain B: Q.220
5 PLIP interactions:4 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:D.165, A:D.204, A:D.247, A:D.247, H2O.26
CA.13: 4 residues within 4Å:- Chain B: D.165, D.204, D.247
- Chain C: Q.220
5 PLIP interactions:4 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:D.165, B:D.204, B:D.247, B:D.247, H2O.39
CA.21: 4 residues within 4Å:- Chain A: Q.220
- Chain C: D.165, D.204, D.247
5 PLIP interactions:3 interactions with chain C, 2 Ligand-Water interactions- Metal complexes: C:D.165, C:D.204, C:D.247, H2O.13, H2O.13
- 3 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)
MRD.11: 5 residues within 4Å:- Chain C: E.182, R.222, V.232, Y.234
- Ligands: MRD.16
5 PLIP interactions:5 interactions with chain C- Hydrophobic interactions: C:V.232, C:Y.234, C:Y.234
- Hydrogen bonds: C:E.182
- Water bridges: C:R.222
MRD.16: 6 residues within 4Å:- Chain B: Q.205, R.245
- Chain C: K.180, Y.234, W.236
- Ligands: MRD.11
8 PLIP interactions:6 interactions with chain C, 2 interactions with chain B- Hydrophobic interactions: C:K.180, C:W.236, C:W.236
- Hydrogen bonds: C:Y.234, C:Y.234, B:R.245
- Water bridges: C:W.236, B:Q.205
MRD.19: 8 residues within 4Å:- Chain B: A.12
- Chain C: R.19, Y.61, V.63, R.93, W.101, A.134, H.136
7 PLIP interactions:7 interactions with chain C- Hydrophobic interactions: C:Y.61, C:V.63, C:W.101, C:A.134
- Hydrogen bonds: C:R.19, C:R.93, C:H.136
- 1 x NI: NICKEL (II) ION(Non-covalent)
- Links
- RCSB PDBe 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
- 2010-03-31
- Peptides
- DISCOIDIN-1 SUBUNIT A: ABC
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
C
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.75 Å
- Oligo State
- homo-trimer
- Ligands
- 3 x NGA: 2-acetamido-2-deoxy-beta-D-galactopyranose(Non-covalent)
- 4 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)
- 7 x SO4: SULFATE ION(Non-functional Binders)
- 3 x CA: CALCIUM ION(Non-covalent)
- 3 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)
- 1 x NI: NICKEL (II) ION(Non-covalent)
- Links
- RCSB PDBe 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
- 2010-03-31
- Peptides
- DISCOIDIN-1 SUBUNIT A: ABC
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
C