SMTL ID : 6obe.1

Ricin A chain bound to VHH antibody V6H8

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

hetero-1-1-mer

Ligands

2 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 3 residues within 4Å: Chain A: H.38, F.265 Ligands: IMD.6 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.38 NI.2: 2 residues within 4Å: Chain A: E.100, H.104 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.100, A:H.104

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

EDO.3: 7 residues within 4Å: Chain A: P.93, D.94, N.95, D.98 Chain B: R.103, Y.104 Ligands: EDO.4 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:R.103, A:D.94, A:D.94, A:D.98, A:D.98 Water bridges: B:Y.104 EDO.4: 6 residues within 4Å: Chain A: R.54, D.73, V.80, D.98 Chain B: Y.104 Ligands: EDO.3 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:Y.104, A:R.54, A:D.73, A:D.73 Water bridges: A:N.76 EDO.5: 6 residues within 4Å: Chain A: E.144, A.145, T.161, R.164, S.165, I.168 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.164 Water bridges: A:E.144, A:E.144, A:A.148

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.6: 7 residues within 4Å: Chain A: H.38, E.39, Q.221, V.243, I.247, F.265 Ligands: NI.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.39

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rudolph, M.J. et al., Intracellular Neutralization of Ricin Toxin by Single-domain Antibodies Targeting the Active Site. J.Mol.Biol. (2020)

Release Date

2020-04-01

Peptides

Ricin A chain: A
VHH antibody V6H8: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ricin A chain

VHH antibody V6H8

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