SMTL ID : 9kx8.1

Mistletoe Lectin I from Viscum album complexed with epimer form of lactose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

hetero-1-1-mer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 9 residues within 4Å: Chain A: F.214, N.215, P.217 Chain B: T.11, V.12, N.44, L.49, N.136 Ligands: NAG.17 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.44 NAG-NAG.2: 5 residues within 4Å: Chain B: W.94, N.96, Y.126, L.228 Ligands: GOL.14 No protein-ligand interaction detected (PLIP)

1 x ZCD- GAL: beta-D-galactopyranose-(1-4)-alpha-D-idopyranose(Non-covalent)

ZCD-GAL.3: 9 residues within 4Å: Chain B: D.23, V.24, R.25, D.26, Q.36, W.38, K.41, N.47, Q.48 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:D.26, B:D.26, B:D.27, B:D.23, B:V.24, B:D.26, B:D.26, B:Q.36, B:K.41, B:K.41, B:N.47, B:Q.48

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: S.148, T.149, R.150 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.148, A:T.149, A:R.150 GOL.5: 7 residues within 4Å: Chain A: Y.191, V.228, T.229, L.230, D.235 Chain B: R.141, P.263 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.141, A:Y.191, A:Y.191, A:D.235 GOL.6: 7 residues within 4Å: Chain A: Y.76, S.114, Y.115, R.125, E.165, R.168, E.196 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.76, A:Y.76, A:R.125, A:E.165, A:E.165, A:R.168, A:E.196 GOL.14: 4 residues within 4Å: Chain B: N.96, V.218, L.228 Ligands: NAG-NAG.2 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.96 GOL.15: 4 residues within 4Å: Chain B: D.235, Q.238, Y.249, N.256 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.238, B:N.256

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

NAG.7: 5 residues within 4Å: Chain A: R.90, D.91, N.112, S.114, D.117 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.90, A:S.114, A:S.114 NAG.16: 3 residues within 4Å: Chain B: D.27, F.29, N.61 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.27 Water bridges: B:F.29 NAG.17: 1 residues within 4Å: Ligands: NAG-NAG.1 No protein-ligand interaction detected (PLIP)

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

SO4.8: 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 SO4.12: 6 residues within 4Å: Chain A: P.93, R.94, G.95, G.96, E.97, T.98 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.95, A:G.95, A:G.96, A:E.97, A:T.98 SO4.18: 5 residues within 4Å: Chain A: W.174, R.175, Q.178 Chain B: Y.146, D.150 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.175

1 x GLY: GLYCINE(Non-covalent)

GLY.9: 2 residues within 4Å: Chain A: Q.134, S.185 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.134, A:S.185

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

CL.10: 2 residues within 4Å: Chain A: S.65, R.143 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain A: S.41, Q.42 Ligand excluded by PLIP

1 x NA: SODIUM ION(Non-functional Binders)

NA.13: 2 residues within 4Å: Chain A: C.247 Chain B: C.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.247

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saeed, A. et al., Mistletoe Lectin I from Viscum album complexed with epimer form of lactose. To Be Published

Release Date

2025-01-15

Peptides

Beta-galactoside-specific lectin 1 chain A isoform 1: A
Beta-galactoside-specific lectin 1 chain B: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Beta-galactoside-specific lectin 1 chain A isoform 1

Beta-galactoside-specific lectin 1 chain B