SMTL ID : 1sz6.1

MISTLETOE LECTIN I FROM VISCUM ALBUM. CRYSTAL STRUCTURE AT 2.05 A RESOLUTION

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

hetero-2-2-mer

Ligands

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

NAG.1: 6 residues within 4Å: Chain A: K.90, D.91, N.112, S.114, D.117, R.120 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.90, A:N.112 NAG.14: 6 residues within 4Å: Chain A: F.214, P.217 Chain B: I.11, V.12, N.44, N.136 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.12 Hydrogen bonds: B:I.11, B:N.44, B:N.44, B:N.136 Water bridges: B:I.11, B:I.11, B:R.13 NAG.15: 5 residues within 4Å: Chain B: W.94, N.96, Y.126, L.228 Ligands: GOL.21 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.126 Water bridges: B:Y.126 NAG.16: 3 residues within 4Å: Chain B: D.27, F.29, N.61 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.29 Hydrogen bonds: B:N.61 Water bridges: B:F.29 NAG.26: 6 residues within 4Å: Chain C: K.90, D.91, N.112, S.114, D.117, R.120 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.90, C:N.112 NAG.39: 6 residues within 4Å: Chain C: F.214, P.217 Chain D: I.11, V.12, N.44, N.136 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:V.12 Hydrogen bonds: D:I.11, D:N.44, D:N.44, D:N.136 Water bridges: D:I.11, D:I.11, D:R.13 NAG.40: 5 residues within 4Å: Chain D: W.94, N.96, Y.126, L.228 Ligands: GOL.46 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:Y.126 NAG.41: 3 residues within 4Å: Chain D: D.27, F.29, N.61 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:F.29 Hydrogen bonds: D:N.61 Water bridges: D:F.29

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

SO4.2: 4 residues within 4Å: Chain A: E.119, H.124, R.125, D.126 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.125, A:D.126, A:D.126 Salt bridges: A:H.124, A:R.125 SO4.27: 4 residues within 4Å: Chain C: E.119, H.124, R.125, D.126 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.125, C:D.126, C:D.126 Salt bridges: C:H.124, C:R.125

6 x AZI: AZIDE ION(Non-covalent)

AZI.3: 6 residues within 4Å: Chain A: D.211, G.212, N.232 Chain B: I.93, L.133, A.134 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.232, A:N.232, B:W.132, B:A.134 AZI.17: 2 residues within 4Å: Chain B: Q.30, D.31 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.30, B:D.31 Water bridges: B:F.29, B:D.31, B:D.31, B:D.31 AZI.18: 4 residues within 4Å: Chain A: R.234 Chain B: W.217, V.218, F.219 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:F.219 Water bridges: B:G.95, A:R.234, A:R.234, A:R.234 AZI.28: 6 residues within 4Å: Chain C: D.211, G.212, N.232 Chain D: I.93, L.133, A.134 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:D.211, C:N.232, D:W.132, D:A.134 AZI.42: 2 residues within 4Å: Chain D: Q.30, D.31 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:Q.30, D:D.31 Water bridges: D:F.29, D:D.31, D:D.31, D:D.31 AZI.43: 4 residues within 4Å: Chain C: R.234 Chain D: W.217, V.218, F.219 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Water bridges: C:R.234, C:R.234, C:R.234, D:G.95 Hydrogen bonds: D:F.219

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

CL.4: 3 residues within 4Å: Chain A: Q.205, H.208, N.216 Ligand excluded by PLIP CL.5: 1 residues within 4Å: Chain A: H.124 Ligand excluded by PLIP CL.29: 3 residues within 4Å: Chain C: Q.205, H.208, N.216 Ligand excluded by PLIP CL.30: 1 residues within 4Å: Chain C: H.124 Ligand excluded by PLIP

30 x GOL: GLYCEROL(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: 6 residues within 4Å: Chain A: G.63, D.64, S.65, G.83, R.143 Ligands: GOL.12 Ligand excluded by PLIP GOL.9: 7 residues within 4Å: Chain A: A.92, P.93, A.94, G.95, A.96, E.97, T.98 Ligand excluded by PLIP GOL.10: 9 residues within 4Å: Chain A: R.175, D.189, Y.191, L.222, P.223, P.224 Chain B: Y.146, V.262, P.263 Ligand excluded by PLIP GOL.11: 5 residues within 4Å: Chain A: P.171, R.175, Q.178 Chain B: Y.146, D.150 Ligand excluded by PLIP GOL.12: 4 residues within 4Å: Chain A: G.83, Q.84, R.143 Ligands: GOL.8 Ligand excluded by PLIP GOL.13: 3 residues within 4Å: Chain A: S.148, T.149, R.150 Ligand excluded by PLIP GOL.19: 6 residues within 4Å: Chain B: D.235, V.236, Q.238, I.247, Y.249, N.256 Ligand excluded by PLIP GOL.20: 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.21: 5 residues within 4Å: Chain B: N.96, N.227, L.228, G.231 Ligands: NAG.15 Ligand excluded by PLIP GOL.22: 4 residues within 4Å: Chain B: A.72, Q.122, T.123 Chain D: Y.68 Ligand excluded by PLIP GOL.23: 4 residues within 4Å: Chain B: T.66, F.79, A.84, V.85 Ligand excluded by PLIP GOL.24: 2 residues within 4Å: Chain B: R.59, N.82 Ligand excluded by PLIP GOL.25: 7 residues within 4Å: Chain A: R.234, D.235, A.238 Chain B: R.141, L.176, F.219, P.261 Ligand excluded by PLIP GOL.31: 3 residues within 4Å: Chain C: Y.1, R.3, L.55 Ligand excluded by PLIP GOL.32: 4 residues within 4Å: Chain C: S.30, S.32, R.41, Q.42 Ligand excluded by PLIP GOL.33: 6 residues within 4Å: Chain C: G.63, D.64, S.65, G.83, R.143 Ligands: GOL.37 Ligand excluded by PLIP GOL.34: 7 residues within 4Å: Chain C: A.92, P.93, A.94, G.95, A.96, E.97, T.98 Ligand excluded by PLIP GOL.35: 9 residues within 4Å: Chain C: R.175, D.189, Y.191, L.222, P.223, P.224 Chain D: Y.146, V.262, P.263 Ligand excluded by PLIP GOL.36: 5 residues within 4Å: Chain C: P.171, R.175, Q.178 Chain D: Y.146, D.150 Ligand excluded by PLIP GOL.37: 4 residues within 4Å: Chain C: G.83, Q.84, R.143 Ligands: GOL.33 Ligand excluded by PLIP GOL.38: 3 residues within 4Å: Chain C: S.148, T.149, R.150 Ligand excluded by PLIP GOL.44: 6 residues within 4Å: Chain D: D.235, V.236, Q.238, I.247, Y.249, N.256 Ligand excluded by PLIP GOL.45: 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.46: 5 residues within 4Å: Chain D: N.96, N.227, L.228, G.231 Ligands: NAG.40 Ligand excluded by PLIP GOL.47: 4 residues within 4Å: Chain B: Y.68 Chain D: A.72, Q.122, T.123 Ligand excluded by PLIP GOL.48: 4 residues within 4Å: Chain D: T.66, F.79, A.84, V.85 Ligand excluded by PLIP GOL.49: 2 residues within 4Å: Chain D: R.59, N.82 Ligand excluded by PLIP GOL.50: 7 residues within 4Å: Chain C: R.234, D.235, A.238 Chain D: R.141, L.176, F.219, P.261 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Gabdoulkhakov, A.G. et al., Crystal Structure of Viscum album Mistletoe Lectin I in native state at 2.05 A resolution, comparison of structure active site conformation in ricin and in viscumin. TO BE PUBLISHED

Release Date

2004-10-05

Peptides

RRNA N-GLYCOSIDASE A CHAIN: AC
BETA-GALACTOSIDE SPECIFIC LECTIN I B CHAIN: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

RRNA N-GLYCOSIDASE A CHAIN

BETA-GALACTOSIDE SPECIFIC LECTIN I B CHAIN

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