SMTL ID : 1onk.1 (1 other biounit)

Mistletoe lectin I from viscum album

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-2-2-mer

Ligands

2 x PO4: PHOSPHATE ION(Post Translational Modification)

PO4.1: 4 residues within 4Å: Chain A: E.119, H.124, R.125, D.126 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.119, A:E.119, A:R.125, A:D.126, A:D.126 Salt bridges: A:H.124, A:R.125 PO4.21: 4 residues within 4Å: Chain C: E.119, H.124, R.125, D.126 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:E.119, C:R.125, C:D.126, C:D.126 Salt bridges: C:H.124, C:R.125

18 x AZI: AZIDE ION(Post Translational Modification)(Non-functional Binders)(Non-covalent)

AZI.2: 2 residues within 4Å: Chain A: R.90, N.112 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.90, A:D.91, A:N.112 AZI.3: 6 residues within 4Å: Chain A: D.211, N.232 Chain B: I.93, W.132, L.133, A.134 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.232, A:N.232, B:W.132, B:A.134 Water bridges: A:R.234 AZI.4: 3 residues within 4Å: Chain A: W.174, Q.178 Chain B: D.150 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.178, A:Q.178 AZI.5: 4 residues within 4Å: Chain A: G.83, D.84, R.143 Ligands: GOL.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.84, A:D.84, A:R.143, A:R.143 AZI.13: 3 residues within 4Å: Chain B: D.27, F.29, N.61 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.27, B:N.61, B:N.61 Water bridges: B:F.29 AZI.14: 2 residues within 4Å: Chain B: H.30, D.31 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.29, B:D.31 Water bridges: B:F.29, B:H.30 AZI.15: 2 residues within 4Å: Chain B: A.84, V.85 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.85 Water bridges: B:T.83 AZI.16: 5 residues within 4Å: Chain A: R.234, I.237 Chain B: W.217, V.218, F.219 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:F.219, B:F.219 Water bridges: A:R.234, A:R.234 AZI.17: 4 residues within 4Å: Chain B: D.235, I.247, Y.249, N.256 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.235, B:D.235, B:N.256 Water bridges: B:S.200, B:Q.257 AZI.22: 2 residues within 4Å: Chain C: R.90, N.112 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.90, C:D.91, C:N.112 AZI.23: 6 residues within 4Å: Chain C: D.211, N.232 Chain D: I.93, W.132, L.133, A.134 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:N.232, C:N.232, D:W.132, D:A.134 Water bridges: C:R.234 AZI.24: 3 residues within 4Å: Chain C: W.174, Q.178 Chain D: D.150 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.178, C:Q.178 AZI.25: 4 residues within 4Å: Chain C: G.83, D.84, R.143 Ligands: GOL.28 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.84, C:D.84, C:R.143, C:R.143 AZI.33: 3 residues within 4Å: Chain D: D.27, F.29, N.61 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.27, D:N.61, D:N.61 Water bridges: D:F.29 AZI.34: 2 residues within 4Å: Chain D: H.30, D.31 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:F.29, D:D.31 Water bridges: D:F.29, D:H.30 AZI.35: 2 residues within 4Å: Chain D: A.84, V.85 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:V.85 Water bridges: D:T.83 AZI.36: 5 residues within 4Å: Chain C: R.234, I.237 Chain D: W.217, V.218, F.219 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:F.219, D:F.219 Water bridges: C:R.234, C:R.234 AZI.37: 4 residues within 4Å: Chain D: D.235, I.247, Y.249, N.256 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.235, D:D.235, D:N.256 Water bridges: D:S.200, D:Q.257

16 x GOL: GLYCEROL(Non-covalent)(Non-functional Binders)

GOL.6: 3 residues within 4Å: Chain A: Y.1, R.3, L.55 Ligand excluded by PLIP GOL.7: 4 residues within 4Å: Chain A: S.30, S.32, R.41, Q.42 Ligand excluded by PLIP GOL.8: 4 residues within 4Å: Chain A: S.65, G.83, R.143 Ligands: AZI.5 Ligand excluded by PLIP GOL.9: 4 residues within 4Å: Chain A: G.95, A.96, E.97, T.98 Ligand excluded by PLIP GOL.10: 6 residues within 4Å: Chain A: R.175, D.189, Y.191, I.222 Chain B: V.262, F.263 Ligand excluded by PLIP GOL.18: 9 residues within 4Å: Chain B: D.23, V.24, R.25, D.26, D.27, Q.36, W.38, K.41, N.47 Ligand excluded by PLIP GOL.19: 5 residues within 4Å: Chain B: N.96, V.218, L.226, L.228 Ligands: NAG.12 Ligand excluded by PLIP GOL.20: 4 residues within 4Å: Chain B: A.72, Q.122, T.123 Chain D: Y.68 Ligand excluded by PLIP GOL.26: 3 residues within 4Å: Chain C: Y.1, R.3, L.55 Ligand excluded by PLIP GOL.27: 4 residues within 4Å: Chain C: S.30, S.32, R.41, Q.42 Ligand excluded by PLIP GOL.28: 4 residues within 4Å: Chain C: S.65, G.83, R.143 Ligands: AZI.25 Ligand excluded by PLIP GOL.29: 4 residues within 4Å: Chain C: G.95, A.96, E.97, T.98 Ligand excluded by PLIP GOL.30: 6 residues within 4Å: Chain C: R.175, D.189, Y.191, I.222 Chain D: V.262, F.263 Ligand excluded by PLIP GOL.38: 9 residues within 4Å: Chain D: D.23, V.24, R.25, D.26, D.27, Q.36, W.38, K.41, N.47 Ligand excluded by PLIP GOL.39: 5 residues within 4Å: Chain D: N.96, V.218, L.226, L.228 Ligands: NAG.32 Ligand excluded by PLIP GOL.40: 4 residues within 4Å: Chain B: Y.68 Chain D: A.72, Q.122, T.123 Ligand excluded by PLIP

4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.11: 8 residues within 4Å: Chain A: F.214, N.215, P.217 Chain B: T.11, V.12, N.44, L.49, N.136 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.12 Hydrogen bonds: B:T.11, B:T.11, B:N.44, B:N.136 Water bridges: B:T.11 NAG.12: 5 residues within 4Å: Chain B: W.94, N.96, Y.126, L.228 Ligands: GOL.19 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.126, B:L.228 NAG.31: 8 residues within 4Å: Chain C: F.214, N.215, P.217 Chain D: T.11, V.12, N.44, L.49, N.136 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:V.12 Hydrogen bonds: D:T.11, D:T.11, D:N.44, D:N.136 Water bridges: D:T.11 NAG.32: 5 residues within 4Å: Chain D: W.94, N.96, Y.126, L.228 Ligands: GOL.39 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:Y.126, D:L.228

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Gabdoulkhakov, A.G. et al., Mistletoe lectin I from viscum album. To be Published

Release Date

2004-02-28

Peptides

Beta-galactoside specific lectin I A chain: AC
Galactose specific lectin I B chain: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Beta-galactoside specific lectin I A chain

Galactose specific lectin I B chain

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