SMTL ID : 4jkx.2 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

hetero-1-1-mer

Ligands

1 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: 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

1 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)

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

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

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(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

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: S.148, T.149, R.150 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.149, A:R.150 Water bridges: A:S.148 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 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:P.171, A:R.175, A:R.175, B:D.150 GOL.10: 3 residues within 4Å: Chain A: G.83, D.84, R.143 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.84, A:D.84, A:R.143, A:R.143 GOL.23: 6 residues within 4Å: Chain B: T.51, K.53, R.59, S.60, N.61, G.62 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.51, B:K.53, B:R.59, B:G.62 Water bridges: B:T.51, B:T.51 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 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:D.23, B:D.26, B:Q.36, B:K.41, B:K.41, B:N.47 Water bridges: B:R.25, B:Q.36 GOL.25: 3 residues within 4Å: Chain B: F.79, A.84, V.85 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.85 GOL.26: 5 residues within 4Å: Chain B: D.235, Q.238, I.247, 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.27: 5 residues within 4Å: Chain B: S.155, N.156, N.171, Q.186 Ligands: GOL.28 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.171, B:Q.186 GOL.28: 5 residues within 4Å: Chain B: S.168, Q.169, Q.170, N.171 Ligands: GOL.27 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.170, B:N.171 GOL.29: 7 residues within 4Å: Chain B: N.96, V.218, L.226, N.227, L.228, G.231 Ligands: NAG-NAG.1 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.96, B:N.227

1 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 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.76 Hydrogen bonds: A:S.114, A:R.125, A:E.165, A:E.196 pi-Cation interactions: A:R.125

6 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: 3 residues within 4Å: Chain B: A.72, Q.122, T.123 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.122, B:T.123, B:T.123 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

1 x DIO: 1,4-DIETHYLENE DIOXIDE(Non-covalent)

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

2 x CL: CHLORIDE ION(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

1 x AZI: AZIDE ION(Non-covalent)

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

Links

RCSB   PDBe   PDBe-KB   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: A
Beta-galactoside-specific lectin 1 B chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Beta-galactoside-specific lectin 1 A chain

Beta-galactoside-specific lectin 1 B chain

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