SMTL ID : 2w95.1

STructure of the Discoidin I from Dictyostelium discoideum in complex with GalNAc at 1.75 angstrom resolution

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)

NGA.1: 6 residues within 4Å: Chain A: Q.214, R.216, W.236, N.237 Chain C: D.207, Y.242 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:Q.214, A:R.216, A:N.237, C:D.207 Water bridges: A:N.237, A:N.237 Salt bridges: A:R.216 NGA.7: 6 residues within 4Å: Chain A: D.207, Y.242 Chain B: Q.214, R.216, W.236, N.237 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:D.207, B:Q.214, B:R.216, B:N.237 Water bridges: A:Y.242, B:W.236, B:N.237 Salt bridges: B:R.216 NGA.15: 6 residues within 4Å: Chain B: D.207, Y.242 Chain C: Q.214, R.216, W.236, N.237 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain C Hydrogen bonds: B:D.207, C:Q.214, C:R.216, C:N.237 Water bridges: B:N.175, C:N.237 Salt bridges: C:R.216

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: 5 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:V.63, A:W.101, C:A.12 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 B, 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: B:S.158, B:T.160, C:T.160, C:T.160, A:S.158 Water bridges: B:S.158, C:S.158, A: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: 2 interactions with chain B, 6 interactions with chain C Hydrogen bonds: B:R.245, C:Y.234, C:Y.234 Water bridges: B:Q.205, C:W.236 Hydrophobic interactions: C:K.180, C:W.236, C:W.236 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)

NI.14: 3 residues within 4Å: Chain A: H.17 Chain B: H.17 Chain C: H.17 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A Metal complexes: C:H.17, B:H.17, A:H.17

Links

RCSB   PDBe   PDBe-KB   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
A

B
B

C
C

DISCOIDIN-1 SUBUNIT A

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