SMTL ID : 2rg9.1

Crystal structure of viscum album mistletoe lectin I in native state at 1.95 A resolution, comparison of structure active site conformation in ricin and in viscumin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

hetero-1-1-mer

Ligands

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

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: 8 residues within 4Å: Chain A: F.214, N.215, P.217 Chain B: I.11, V.12, N.44, L.49, N.136 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.12 Hydrogen bonds: B:I.11, B:I.11, B:N.44, B:N.44, B:N.136 Water bridges: 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 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.126, B:L.228 Hydrogen bonds: B:N.96 Water bridges: B:N.96, B:Y.126, 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

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

SO4.2: 4 residues within 4Å: Chain A: E.119, H.124, R.125, D.126 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.119, A:R.125, A:D.126, A:D.126 Salt bridges: A:H.124, A:R.125

3 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 B, 2 interactions with chain A Hydrogen bonds: B:W.132, B:A.134, A:D.211, A:N.232 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: 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 Water bridges: B:G.95, A:R.234, A:R.234

2 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: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

15 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 3 residues within 4Å: Chain A: Y.1, R.3, L.55 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.1, A:R.3 Water bridges: A:Y.1 GOL.7: 3 residues within 4Å: Chain A: S.32, R.41, Q.42 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.30, A:S.32, A:S.32, A:R.41, A:R.41, A:Q.42, A:Q.42 GOL.8: 6 residues within 4Å: Chain A: G.63, D.64, S.65, G.83, R.143 Ligands: GOL.12 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.63, A:S.65, A:R.143 Water bridges: A:Q.81, A:Q.81 GOL.9: 6 residues within 4Å: Chain A: P.93, R.94, G.95, A.96, E.97, T.98 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.95, A:E.97, A:T.98 GOL.10: 7 residues within 4Å: Chain A: R.175, D.189, Y.191, L.222, P.223 Chain B: V.262, P.263 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Y.146, B:Y.146, A:R.175, A:R.175 GOL.11: 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:R.175, A:R.175, B:D.150 GOL.12: 4 residues within 4Å: Chain A: G.83, Q.84, R.143 Ligands: GOL.8 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.84, A:Q.84, A:Q.84, A:R.143, A:R.143 GOL.13: 3 residues within 4Å: Chain A: S.148, T.149, R.150 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.148, A:S.148, A:T.149, A:T.149, A:R.150 GOL.19: 5 residues within 4Å: Chain B: D.235, V.236, Q.238, Y.249, N.256 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.235, B:Q.238, B:N.256 Water bridges: B:N.254 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 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:D.23, B:D.26, B:D.27, B:Q.36, B:K.41, B:K.41, B:N.47 Water bridges: B:R.25, B:Q.36 GOL.21: 5 residues within 4Å: Chain B: N.96, L.226, N.227, L.228 Ligands: NAG.15 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.227 GOL.22: 3 residues within 4Å: Chain B: A.72, Q.122, T.123 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.122, B:T.123, B:T.123 Water bridges: B:A.72 GOL.23: 5 residues within 4Å: Chain B: T.66, M.77, F.79, A.84, V.85 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.85 GOL.24: 2 residues within 4Å: Chain B: R.59, N.82 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.59, B:R.59, B:N.82 Water bridges: B:C.81 GOL.25: 7 residues within 4Å: Chain A: R.234, D.235 Chain B: R.141, V.143, L.176, F.219, P.261 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.235, B:R.141 Water bridges: A:D.235

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Karpechenko, N.U. et al., Crystal structure of viscum album mistletoe lectin I in native state at 1.95 A resolution, comparison of structure active site conformation in ricin and in viscumin. To be Published

Release Date

2008-10-07

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