SMTL ID : 3rtj.1

Crystal structure of ricin bound with dinucleotide ApG

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-1-1-mer

Ligands

1 x A- G: RNA (5'-R(*AP*G)-3')(Non-covalent)

A-G.1: 16 residues within 4Å: Chain A: A.79, Y.80, V.81, F.93, D.96, G.121, N.122, Y.123, D.124, I.172, S.176, E.177, R.180, E.208, N.209, W.211 Protein-ligand interaction information (PLIP) not available

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

BGC-GAL.2: 9 residues within 4Å: Chain B: D.22, V.23, R.24, D.25, Q.35, W.37, K.40, N.46, Q.47 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:D.25, B:D.25, B:D.25, B:D.22, B:D.25, B:D.25, B:Q.35, B:Q.35, B:K.40, B:K.40, B:N.46, B:Q.47 BGC-GAL.3: 9 residues within 4Å: Chain B: E.199, D.234, V.235, R.236, A.237, I.246, Y.248, H.251, N.255 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.199, B:D.234, B:A.237, B:H.251, B:N.255

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.4: 5 residues within 4Å: Chain B: Q.91, W.93, N.95, Y.125, L.227 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.93 NAG-NAG.5: 8 residues within 4Å: Chain A: F.226, A.227, P.229, Y.243 Chain B: I.10, T.43, L.48, N.135 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.43, B:L.48

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Monzingo, A.F. et al., X-ray analysis of substrate analogs in the ricin A-chain active site. J.Mol.Biol. (1992)

Release Date

2011-08-31

Peptides

Ricin A chain: A
Ricin B chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ricin A chain

Ricin B chain

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