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

Crystal structure Mistletoe Lectin I from Viscum album in complex with kinetin at 2.35 A resolution.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 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(Non-functional Binders)

NAG-NAG.1: 6 residues within 4Å: Chain B: E.92, W.94, N.96, Y.126, L.228 Ligands: GOL.29 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.94 NAG-NAG.31: 6 residues within 4Å: Chain D: E.92, W.94, N.96, Y.126, L.228 Ligands: GOL.59 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:W.94

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

NAG-NAG-NAG.2: 8 residues within 4Å: Chain A: F.214, N.215, P.217 Chain B: T.11, V.12, N.44, L.49, N.136 No protein-ligand interaction detected (PLIP) NAG-NAG-NAG.32: 8 residues within 4Å: Chain C: F.214, N.215, P.217 Chain D: T.11, V.12, N.44, L.49, N.136 No protein-ligand interaction detected (PLIP)

10 x SO4: SULFATE ION(Non-functional Binders)(Non-covalent)

SO4.3: 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 SO4.11: 4 residues within 4Å: Chain A: Q.205, H.208, N.215, N.216 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.205, A:N.215, A:N.216 Water bridges: A:Q.205, A:N.215 Salt bridges: A:H.208 SO4.12: 3 residues within 4Å: Chain A: R.7, T.9, Q.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.11 Salt bridges: A:R.7 SO4.13: 3 residues within 4Å: Chain A: G.123, H.124, R.150 5 PLIP interactions: 5 interactions with chain A Water bridges: A:G.123, A:H.124, A:R.150 Salt bridges: A:H.124, A:R.150 SO4.14: 5 residues within 4Å: Chain A: P.93, A.94, G.95, A.96, E.97 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.93, A:G.95, A:A.96, A:E.97 SO4.33: 5 residues within 4Å: Chain C: Y.115, E.119, H.124, R.125, D.126 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.125, C:D.126 Salt bridges: C:H.124, C:R.125 SO4.41: 4 residues within 4Å: Chain C: Q.205, H.208, N.215, N.216 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Q.205, C:N.215, C:N.216 Water bridges: C:Q.205, C:N.215 Salt bridges: C:H.208 SO4.42: 3 residues within 4Å: Chain C: R.7, T.9, Q.11 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.9, C:Q.11 Salt bridges: C:R.7 SO4.43: 3 residues within 4Å: Chain C: G.123, H.124, R.150 5 PLIP interactions: 5 interactions with chain C Water bridges: C:G.123, C:H.124, C:R.150 Salt bridges: C:H.124, C:R.150 SO4.44: 5 residues within 4Å: Chain C: P.93, A.94, G.95, A.96, E.97 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:P.93, C:G.95, C:A.96, C:E.97, C:E.97

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

NAG.4: 6 residues within 4Å: Chain A: K.90, D.91, N.112, S.114, D.117, R.120 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.112, A:S.114, A:S.114 NAG.17: 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:D.27 NAG.34: 6 residues within 4Å: Chain C: K.90, D.91, N.112, S.114, D.117, R.120 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.91, C:N.112, C:S.114, C:S.114 NAG.47: 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:D.27

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

GOL.5: 3 residues within 4Å: Chain A: S.148, T.149, R.150 Ligand excluded by PLIP GOL.6: 8 residues within 4Å: Chain A: P.171, W.174, R.175, Q.178 Chain B: Y.146, D.150, L.260 Ligands: AZI.16 Ligand excluded by PLIP GOL.10: 3 residues within 4Å: Chain A: G.83, D.84, R.143 Ligand excluded by PLIP GOL.23: 6 residues within 4Å: Chain B: T.51, K.53, R.59, S.60, N.61, G.62 Ligand excluded by PLIP GOL.24: 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.25: 3 residues within 4Å: Chain B: F.79, A.84, V.85 Ligand excluded by PLIP GOL.26: 5 residues within 4Å: Chain B: D.235, Q.238, I.247, Y.249, N.256 Ligand excluded by PLIP GOL.27: 5 residues within 4Å: Chain B: S.155, N.156, N.171, Q.186 Ligands: GOL.28 Ligand excluded by PLIP GOL.28: 5 residues within 4Å: Chain B: S.168, Q.169, Q.170, N.171 Ligands: GOL.27 Ligand excluded by PLIP GOL.29: 7 residues within 4Å: Chain B: N.96, V.218, L.226, N.227, L.228, G.231 Ligands: NAG-NAG.1 Ligand excluded by PLIP GOL.35: 3 residues within 4Å: Chain C: S.148, T.149, R.150 Ligand excluded by PLIP GOL.36: 8 residues within 4Å: Chain C: P.171, W.174, R.175, Q.178 Chain D: Y.146, D.150, L.260 Ligands: AZI.46 Ligand excluded by PLIP GOL.40: 3 residues within 4Å: Chain C: G.83, D.84, R.143 Ligand excluded by PLIP GOL.53: 6 residues within 4Å: Chain D: T.51, K.53, R.59, S.60, N.61, G.62 Ligand excluded by PLIP GOL.54: 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.55: 3 residues within 4Å: Chain D: F.79, A.84, V.85 Ligand excluded by PLIP GOL.56: 5 residues within 4Å: Chain D: D.235, Q.238, I.247, Y.249, N.256 Ligand excluded by PLIP GOL.57: 5 residues within 4Å: Chain D: S.155, N.156, N.171, Q.186 Ligands: GOL.58 Ligand excluded by PLIP GOL.58: 5 residues within 4Å: Chain D: S.168, Q.169, Q.170, N.171 Ligands: GOL.57 Ligand excluded by PLIP GOL.59: 7 residues within 4Å: Chain D: N.96, V.218, L.226, N.227, L.228, G.231 Ligands: NAG-NAG.31 Ligand excluded by PLIP

2 x H35: N-(FURAN-2-YLMETHYL)-7H-PURIN-6-AMINE(Non-covalent)

H35.7: 14 residues within 4Å: Chain A: Y.76, G.113, S.114, Y.115, L.118, E.119, R.125, L.157, I.160, Q.161, E.165, R.168, E.196, T.197 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.76 Hydrogen bonds: A:R.125, A:E.165, A:E.196 pi-Cation interactions: A:R.125 H35.37: 14 residues within 4Å: Chain C: Y.76, G.113, S.114, Y.115, L.118, E.119, R.125, L.157, I.160, Q.161, E.165, R.168, E.196, T.197 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:Y.76 Hydrogen bonds: C:R.125 pi-Cation interactions: C:R.125

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

EDO.8: 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 EDO.18: 4 residues within 4Å: Chain B: A.72, Q.122, T.123 Chain D: Y.68 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:Q.122, B:T.123, B:T.123, D:Y.68 Water bridges: D:Y.68 EDO.19: 6 residues within 4Å: Chain A: R.234 Chain B: L.133, R.141, L.176, Y.177, G.178 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.141 Water bridges: B:Y.177, B:G.180 EDO.20: 3 residues within 4Å: Chain B: S.8, E.9, K.54 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.8, B:E.9, B:K.54 EDO.21: 3 residues within 4Å: Chain B: Q.190, V.206, S.207 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.190, B:S.207 EDO.22: 2 residues within 4Å: Chain B: H.30, D.31 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.30, B:D.31, B:D.31 EDO.38: 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 EDO.48: 4 residues within 4Å: Chain B: Y.68 Chain D: A.72, Q.122, T.123 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:Q.122, D:T.123, D:T.123, B:Y.68, B:Y.68 EDO.49: 6 residues within 4Å: Chain C: R.234 Chain D: L.133, R.141, L.176, Y.177, G.178 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.141 Water bridges: D:Y.177, D:G.180 EDO.50: 3 residues within 4Å: Chain D: S.8, E.9, K.54 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.8, D:E.9, D:K.54 EDO.51: 3 residues within 4Å: Chain D: Q.190, V.206, S.207 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.190, D:S.207 EDO.52: 2 residues within 4Å: Chain D: H.30, D.31 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.31, D:D.31

2 x DIO: 1,4-DIETHYLENE DIOXIDE(Non-functional Binders)

DIO.9: 4 residues within 4Å: Chain A: S.30, S.32, R.41, Q.42 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.41, A:Q.42, A:Q.42 DIO.39: 4 residues within 4Å: Chain C: S.30, S.32, R.41, Q.42 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.41, C:Q.42, C:Q.42

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

CL.15: 4 residues within 4Å: Chain A: T.9, H.10, Q.11, A.61 Ligand excluded by PLIP CL.30: 3 residues within 4Å: Chain B: M.20, I.114, K.115 Ligand excluded by PLIP CL.45: 4 residues within 4Å: Chain C: T.9, H.10, Q.11, A.61 Ligand excluded by PLIP CL.60: 3 residues within 4Å: Chain D: M.20, I.114, K.115 Ligand excluded by PLIP

2 x AZI: AZIDE ION

AZI.16: 5 residues within 4Å: Chain A: Q.178 Chain B: Y.146, D.150, C.165 Ligands: GOL.6 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.178, A:Q.178, B:D.150 AZI.46: 5 residues within 4Å: Chain C: Q.178 Chain D: Y.146, D.150, C.165 Ligands: GOL.36 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:Q.178, C:Q.178, D:D.150

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Prokofev, I.I. et al., Crystal structure Mistletoe Lectin I from Viscum album in complex with kinetin at 2.35 A resolution. To be Published

Release Date

2014-05-21

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Beta-galactoside-specific lectin 1 A chain

Beta-galactoside-specific lectin 1 B chain

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