SMTL ID : 4eb2.1 (1 other biounit)

Crystal structure Mistletoe Lectin I from Viscum album in complex with n-acetyl-d-glucosamine at 1.94 A resolution.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

hetero-2-2-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: 8 residues within 4Å: Chain A: F.214, N.215, P.217 Chain B: I.11, V.12, N.44, L.49, N.136 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.11 NAG-NAG.28: 8 residues within 4Å: Chain C: F.214, N.215, P.217 Chain D: I.11, V.12, N.44, L.49, N.136 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:I.11

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

NAG.2: 5 residues within 4Å: Chain A: K.90, D.91, N.112, S.114, D.117 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.90, 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 Hydrophobic interactions: B:F.29 Water bridges: B:F.29 NAG.17: 5 residues within 4Å: Chain B: W.94, N.96, Y.126, L.228 Ligands: PEG.26 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.126, B:L.228 NAG.29: 5 residues within 4Å: Chain C: K.90, D.91, N.112, S.114, D.117 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.90, C:D.91, C:S.114 NAG.43: 3 residues within 4Å: Chain D: D.27, F.29, N.61 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.29 Water bridges: D:F.29 NAG.44: 5 residues within 4Å: Chain D: W.94, N.96, Y.126, L.228 Ligands: PEG.53 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:Y.126, D:L.228

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

SO4.3: 5 residues within 4Å: Chain A: E.119, H.124, R.125, D.126 Ligands: PEG.14 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.119, A:R.125, A:D.126 Salt bridges: A:H.124, A:R.125 SO4.4: 3 residues within 4Å: Chain A: Q.205, H.208, N.216 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.205, A:N.216 Water bridges: A:Q.205, A:N.215 Salt bridges: A:H.208 SO4.30: 5 residues within 4Å: Chain C: E.119, H.124, R.125, D.126 Ligands: PEG.41 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:E.119, C:E.119, C:R.125, C:D.126 Salt bridges: C:H.124, C:R.125 SO4.31: 3 residues within 4Å: Chain C: Q.205, H.208, N.216 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.205, C:N.216 Water bridges: C:Q.205, C:N.215 Salt bridges: C:H.208

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: Q.148, T.149, R.150 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.149, A:R.150 GOL.6: 6 residues within 4Å: Chain A: P.171, R.175, Q.178 Chain B: Y.146, D.150, V.262 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.150, A:P.171, A:R.175, A:R.175 GOL.7: 4 residues within 4Å: Chain A: G.63, D.64, S.65, R.143 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.63, A:S.65, A:R.143 Water bridges: A:G.83 GOL.8: 6 residues within 4Å: Chain A: R.175, D.189, Y.191, L.222 Chain B: Y.146, P.263 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.175, B:Y.146 GOL.18: 8 residues within 4Å: Chain B: D.23, V.24, R.25, D.26, Q.36, W.38, K.41, N.47 7 PLIP interactions: 7 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 GOL.19: 4 residues within 4Å: Chain B: M.77, F.79, A.84, V.85 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.85 GOL.20: 3 residues within 4Å: Chain B: E.87, P.102, R.103 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.87, B:R.103, B:R.103 GOL.32: 3 residues within 4Å: Chain C: Q.148, T.149, R.150 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.149, C:T.149, C:R.150 GOL.33: 6 residues within 4Å: Chain C: P.171, R.175, Q.178 Chain D: Y.146, D.150, V.262 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:D.150, C:P.171, C:R.175, C:R.175 GOL.34: 4 residues within 4Å: Chain C: G.63, D.64, S.65, R.143 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.63, C:S.65, C:R.143 Water bridges: C:G.83 GOL.35: 6 residues within 4Å: Chain C: R.175, D.189, Y.191, L.222 Chain D: Y.146, P.263 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:R.175, D:Y.146, D:Y.146 GOL.45: 8 residues within 4Å: Chain D: D.23, V.24, R.25, D.26, Q.36, W.38, K.41, N.47 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:D.23, D:D.26, D:D.27, D:Q.36, D:K.41, D:K.41, D:N.47 GOL.46: 4 residues within 4Å: Chain D: M.77, F.79, A.84, V.85 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:V.85 GOL.47: 3 residues within 4Å: Chain D: E.87, P.102, R.103 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.103, D:R.103

10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.9: 5 residues within 4Å: Chain A: Y.76, G.113, Y.115, I.160, R.168 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.168, A:R.168 Water bridges: A:G.113 EDO.21: 3 residues within 4Å: Chain B: E.142, R.173, K.185 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.173 Water bridges: B:E.170, B:R.173 EDO.22: 4 residues within 4Å: Chain B: T.51, K.53, R.59, G.62 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.51, B:R.59, B:G.62 Water bridges: B:G.62 EDO.23: 4 residues within 4Å: Chain B: S.200, A.237, R.245, I.247 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.200, B:R.245 EDO.24: 3 residues within 4Å: Chain B: F.29, Q.30, D.31 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.29, B:D.31 EDO.36: 5 residues within 4Å: Chain C: Y.76, G.113, Y.115, I.160, R.168 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.168, C:R.168 Water bridges: C:G.113 EDO.48: 3 residues within 4Å: Chain D: E.142, R.173, K.185 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.173 Water bridges: D:E.170, D:R.173 EDO.49: 4 residues within 4Å: Chain D: T.51, K.53, R.59, G.62 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:T.51, D:T.51, D:R.59, D:G.62 Water bridges: D:G.62 EDO.50: 4 residues within 4Å: Chain D: S.200, A.237, R.245, I.247 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.200, D:R.245 EDO.51: 3 residues within 4Å: Chain D: F.29, Q.30, D.31 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:F.29, D:D.31

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

CL.10: 4 residues within 4Å: Chain A: T.13, G.14, A.15, N.181 Ligand excluded by PLIP CL.37: 4 residues within 4Å: Chain C: T.13, G.14, A.15, N.181 Ligand excluded by PLIP

14 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.11: 3 residues within 4Å: Chain A: S.30, R.41, Q.42 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.41, A:R.41, A:Q.42, A:Q.42 PEG.12: 3 residues within 4Å: Chain A: G.95, A.96, E.97 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.95, A:E.97 PEG.13: 4 residues within 4Å: Chain A: Q.178, Y.179, S.182, A.184 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.178, A:S.182, A:S.182 PEG.14: 3 residues within 4Å: Chain A: H.124, D.126 Ligands: SO4.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.124 PEG.25: 4 residues within 4Å: Chain B: N.18, Y.177, R.183, Q.188 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.18, B:Y.177, B:R.183 PEG.26: 4 residues within 4Å: Chain B: N.96, L.226, L.228 Ligands: NAG.17 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.96, B:L.228 PEG.27: 5 residues within 4Å: Chain B: D.55, R.59, C.81, N.82, R.86 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.59, B:R.59, B:C.81, B:R.86 PEG.38: 3 residues within 4Å: Chain C: S.30, R.41, Q.42 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.41, C:R.41, C:Q.42, C:Q.42 PEG.39: 3 residues within 4Å: Chain C: G.95, A.96, E.97 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.95, C:E.97 PEG.40: 4 residues within 4Å: Chain C: Q.178, Y.179, S.182, A.184 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.178, C:S.182, C:S.182 PEG.41: 3 residues within 4Å: Chain C: H.124, D.126 Ligands: SO4.30 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.124, C:D.126 PEG.52: 4 residues within 4Å: Chain D: N.18, Y.177, R.183, Q.188 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.18, D:R.183 PEG.53: 4 residues within 4Å: Chain D: N.96, L.226, L.228 Ligands: NAG.44 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.96, D:L.228 PEG.54: 5 residues within 4Å: Chain D: D.55, R.59, C.81, N.82, R.86 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.59, D:R.59, D:C.81, D:R.86

2 x AZI: AZIDE ION(Non-covalent)

AZI.15: 4 residues within 4Å: Chain A: D.211 Chain B: K.53, K.54, G.56 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.56 AZI.42: 4 residues within 4Å: Chain C: D.211 Chain D: K.53, K.54, G.56 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.54, D:G.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Laskov, A.A. et al., Crystal structure Mistletoe Lectin I from Viscum album in complex with N-acetyl-D-glucosamine at 1.94 A resolution. To be Published

Release Date

2013-03-27

Peptides

Beta-galactoside-specific lectin 1 chain A: AC
Beta-galactoside-specific lectin 1 chain B: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Beta-galactoside-specific lectin 1 chain A

Beta-galactoside-specific lectin 1 chain B

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