SMTL ID : 3o5w.1

Binding of kinetin in the active site of mistletoe lectin I

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-1-1-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: 4 residues within 4Å: Chain B: W.94, N.96, Y.126, L.228 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain B: D.27, F.29, N.61 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-NAG.2: 7 residues within 4Å: Chain A: F.214, P.217 Chain B: T.11, V.12, N.44, L.49, N.136 No protein-ligand interaction detected (PLIP)

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

SO4.4: 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

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

NAG.5: 4 residues within 4Å: Chain A: D.91, N.112, S.114, D.117 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.91, A:D.91

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 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:T.149, A:R.150 GOL.7: 8 residues within 4Å: Chain A: P.171, W.174, R.175, Q.178 Chain B: Y.146, D.150, L.260, V.262 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:P.171, A:R.175, B:D.150 Water bridges: A:R.175 GOL.9: 7 residues within 4Å: Chain A: R.234, D.235 Chain B: L.133, R.141, L.176, Y.177 Ligands: GOL.13 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:L.176, A:D.235, A:D.235 GOL.10: 4 residues within 4Å: Chain A: G.83, D.84, Q.85, R.143 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.84, A:R.143 Water bridges: A:R.143, A:R.143 GOL.11: 9 residues within 4Å: Chain B: D.23, V.24, R.25, D.26, Q.36, W.38, K.41, N.47, Q.48 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:D.23, B:D.26, B:Q.36, B:K.41, B:K.41, B:N.47, B:Q.48 Water bridges: B:R.25, B:Q.36 GOL.12: 5 residues within 4Å: Chain B: M.77, F.79, T.83, A.84, V.85 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.85 GOL.13: 6 residues within 4Å: Chain A: R.234 Chain B: G.95, W.217, V.218, F.219 Ligands: GOL.9 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.96, B:W.217, B:F.219, B:F.219 Water bridges: A:R.234 GOL.14: 3 residues within 4Å: Chain B: F.29, H.30, D.31 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.31, B:D.31

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

H35.8: 10 residues within 4Å: Chain A: Y.76, G.113, Y.115, E.119, R.125, L.157, I.160, E.165, R.168, E.196 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.157, A:E.196 Hydrogen bonds: A:Y.115, A:R.168, A:R.168

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malecki, P.H. et al., Binding of the plant hormone kinetin in the active site of Mistletoe Lectin I from Viscum album. Biochim.Biophys.Acta (2012)

Release Date

2011-09-14

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