SMTL ID : 1yf8.1

Crystal structure of Himalayan mistletoe RIP reveals the presence of a natural inhibitor and a new functionally active sugar-binding site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 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: 2 residues within 4Å: Chain B: W.90, N.92 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- MAN- BMA: beta-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG-MAN-BMA.2: 6 residues within 4Å: Chain A: F.208, P.211 Chain B: T.7, N.40, L.45, N.132 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-MAN.3: 4 residues within 4Å: Chain B: D.23, F.25, P.42, N.57 No protein-ligand interaction detected (PLIP)

2 x BGC- GAL: beta-D-galactopyranose-(1-4)-beta-D-glucopyranose(Non-covalent)

BGC-GAL.4: 5 residues within 4Å: Chain B: D.229, V.230, I.239, Y.241, N.248 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.229, B:V.230, B:N.248 BGC-GAL.5: 10 residues within 4Å: Chain B: T.62, T.63, Y.64, Y.66, Y.71, M.73, F.75, A.80, V.81, A.84 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.66, B:V.81

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

NAG.6: 1 residues within 4Å: Chain A: N.107 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.107

1 x P6C: 2-AMINO-4-ISOPROPYL-PTERIDINE-6-CARBOXYLIC ACID(Non-covalent)

P6C.7: 7 residues within 4Å: Chain A: Y.75, G.108, S.109, Y.110, R.162, W.193, G.194 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.75, A:Y.110 Salt bridges: A:R.162

1 x GAL: beta-D-galactopyranose(Non-covalent)

GAL.8: 8 residues within 4Å: Chain B: D.19, R.21, D.22, D.23, Q.32, W.34, K.37, N.43 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.22, B:D.23, B:Q.32, B:K.37, B:K.37, B:N.43

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mishra, V. et al., Crystal structure of himalayan mistletoe ribosome-inactivating protein reveals the presence of a natural inhibitor and a new functionally active sugar-binding site. J.Biol.Chem. (2005)

Release Date

2005-03-08

Peptides

Beta-galactoside-specific lectin 4: A
Beta-galactoside-specific lectin 4: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Beta-galactoside-specific lectin 4

Beta-galactoside-specific lectin 4

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