SMTL ID : 2r9k.1 (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-1-1-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: D.91, N.112, S.114 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.112, A:S.114, A:S.114 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: 5 residues within 4Å: Chain B: W.94, N.96, Y.126, L.228 Ligands: NAG.11 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.126 Water bridges: B:N.96 NAG.11: 2 residues within 4Å: Chain B: W.94 Ligands: NAG.10 No protein-ligand interaction detected (PLIP) NAG.12: 9 residues within 4Å: Chain A: F.214, N.215, P.217 Chain B: I.11, V.12, N.44, L.49, N.136 Ligands: NAG.13 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.13: 4 residues within 4Å: Chain B: I.11, N.44, L.49 Ligands: NAG.12 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.49

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

SO4.2: 2 residues within 4Å: Chain A: R.41, Q.42 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.42, A:Q.42 Salt bridges: A:R.41 SO4.3: 5 residues within 4Å: Chain A: Y.115, E.119, H.124, R.125, D.126 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.125, A:D.126 Salt bridges: A:H.124, A:R.125 SO4.4: 5 residues within 4Å: Chain A: T.204, Q.205, H.208, N.215, N.216 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.205, A:N.216 Salt bridges: A:H.208 SO4.14: 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

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: R.25, N.170, W.174 Chain B: N.221, E.222, G.223, M.258 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.222, A:W.174 GOL.6: 6 residues within 4Å: Chain A: P.171, W.174, R.175, Q.178 Chain B: Y.146, D.150 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:P.171, A:R.175, B:D.150 GOL.15: 6 residues within 4Å: Chain A: R.234 Chain B: N.96, W.217, V.218, F.219 Ligands: GOL.16 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.96, B:F.219, B:F.219 GOL.16: 9 residues within 4Å: Chain A: R.234, D.235 Chain B: L.133, R.141, L.176, Y.177, G.178 Ligands: SGI.8, GOL.15 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.234, B:Y.177

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

CL.7: 2 residues within 4Å: Chain A: G.123, K.150 Ligand excluded by PLIP

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

SGI.8: 11 residues within 4Å: Chain A: V.228, T.229, R.234, D.235 Chain B: R.141, E.142, T.143, L.176, P.261, P.263 Ligands: GOL.16 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:R.141, B:T.143, B:P.263, A:V.228, A:V.228 Hydrogen bonds: A:R.234 Water bridges: A:T.229

Links

RCSB   PDBe   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: A
Beta-galactoside-specific lectin 1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Beta-galactoside-specific lectin 1

Beta-galactoside-specific lectin 1

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