SMTL ID : 2r9k.3 (2 other biounits)

Crystal Structure of Misteltoe Lectin I in Complex with Phloretamide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-2-2-mer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(4-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 4 residues within 4Å: Chain A: W.94, N.96, Y.126, L.228 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain B: W.94, N.96, Y.126, L.228 No protein-ligand interaction detected (PLIP)

8 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Post Translational Modification)

NAG.2: 2 residues within 4Å: Chain A: F.29, N.61 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.29 Hydrogen bonds: A:N.61, A:N.61 Water bridges: A:F.29 NAG.3: 6 residues within 4Å: Chain A: I.11, V.12, N.44, L.49, N.136 Ligands: NAG.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.12 Hydrogen bonds: A:I.11, A:I.11, A:N.44, A:N.136 Water bridges: A:I.11 NAG.4: 4 residues within 4Å: Chain A: I.11, N.44, L.49 Ligands: NAG.3 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.49 NAG.9: 2 residues within 4Å: Chain B: F.29, N.61 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.29 Hydrogen bonds: B:N.61, B:N.61 Water bridges: B:F.29 NAG.10: 6 residues within 4Å: Chain B: I.11, V.12, N.44, L.49, N.136 Ligands: NAG.11 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.12 Hydrogen bonds: B:I.11, B:I.11, B:N.44, B:N.136 Water bridges: B:I.11 NAG.11: 4 residues within 4Å: Chain B: I.11, N.44, L.49 Ligands: NAG.10 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.49 NAG.15: 3 residues within 4Å: Chain C: D.91, N.112, S.114 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.112, C:S.114, C:S.114 NAG.23: 3 residues within 4Å: Chain D: D.91, N.112, S.114 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.91, D:S.114, D:S.114

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 9 residues within 4Å: Chain A: D.23, V.24, R.25, D.26, D.27, Q.36, W.38, K.41, N.47 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.26, A:D.27, A:Q.36 Salt bridges: A:K.41 SO4.12: 9 residues within 4Å: Chain B: D.23, V.24, R.25, D.26, D.27, Q.36, W.38, K.41, N.47 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.26, B:D.27, B:Q.36 Salt bridges: B:K.41 SO4.16: 2 residues within 4Å: Chain C: R.41, Q.42 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.42, C:Q.42 Salt bridges: C:R.41 SO4.17: 5 residues within 4Å: Chain C: Y.115, E.119, H.124, R.125, D.126 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.125, C:D.126 Salt bridges: C:H.124, C:R.125 SO4.18: 5 residues within 4Å: Chain C: T.204, Q.205, H.208, N.215, N.216 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.205, C:N.216 Salt bridges: C:H.208 SO4.24: 2 residues within 4Å: Chain D: R.41, Q.42 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.42, D:Q.42 Salt bridges: D:R.41 SO4.25: 5 residues within 4Å: Chain D: Y.115, E.119, H.124, R.125, D.126 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:Y.115, D:E.119, D:R.125, D:D.126 Salt bridges: D:H.124, D:R.125 SO4.26: 5 residues within 4Å: Chain D: T.204, Q.205, H.208, N.215, N.216 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.205, D:N.216 Salt bridges: D:H.208

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: N.96, W.217, V.218, F.219 Ligands: GOL.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.96, A:F.219, A:F.219 GOL.7: 6 residues within 4Å: Chain A: L.133, R.141, L.176, Y.177, G.178 Ligands: GOL.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.177 GOL.13: 5 residues within 4Å: Chain B: N.96, W.217, V.218, F.219 Ligands: GOL.14 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.96, B:F.219, B:F.219 GOL.14: 6 residues within 4Å: Chain B: L.133, R.141, L.176, Y.177, G.178 Ligands: GOL.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.177 GOL.19: 3 residues within 4Å: Chain C: R.25, N.170, W.174 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:W.174 GOL.20: 4 residues within 4Å: Chain C: P.171, W.174, R.175, Q.178 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:P.171, C:R.175 GOL.27: 3 residues within 4Å: Chain D: R.25, N.170, W.174 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:W.174 GOL.28: 4 residues within 4Å: Chain D: P.171, W.174, R.175, Q.178 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:P.171, D:R.175

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

CL.21: 3 residues within 4Å: Chain C: G.123, K.150 Ligands: CL.29 Ligand excluded by PLIP CL.29: 3 residues within 4Å: Chain D: G.123, K.150 Ligands: CL.21 Ligand excluded by PLIP

2 x SGI: 3-(4-hydroxyphenyl)propanamide(Non-covalent)

SGI.22: 4 residues within 4Å: Chain C: V.228, T.229, R.234, D.235 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:V.228, C:V.228 Hydrogen bonds: C:R.234 Water bridges: C:T.229 SGI.30: 4 residues within 4Å: Chain D: V.228, T.229, R.234, D.235 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:V.228, D:V.228 Hydrogen bonds: D:R.234 Water bridges: D:T.229

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meyer, A. et al., The mistletoe lectin I--phloretamide structure reveals a new function of plant lectins. Biochem.Biophys.Res.Commun. (2007)

Release Date

2007-10-30

Peptides

Beta-galactoside-specific lectin 1 chain B: AB
Beta-galactoside-specific lectin 1: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

C
A

D
A

Beta-galactoside-specific lectin 1 chain B

Beta-galactoside-specific lectin 1

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