SMTL ID : 4z9k.1

Ricin A chain bound to camelid nanobody (VHH2)(F5)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

hetero-1-1-mer

Ligands

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

EDO.1: 7 residues within 4Å: Chain A: Q.109, R.111, Y.112 Chain B: L.3, A.92, S.93, R.94 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.93, B:R.94, A:Q.109, A:R.111 Water bridges: B:R.94 EDO.2: 4 residues within 4Å: Chain A: G.128, N.129, L.130, N.133 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.130, A:L.130, A:N.133

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 3 residues within 4Å: Chain A: E.99, H.103 Ligands: CL.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.99, A:H.103

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 3 residues within 4Å: Chain A: E.99, H.103 Ligands: ZN.3 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: L.130, R.131, E.132, I.202 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rudolph, M.J. et al., Structural analysis of nested neutralizing and non-neutralizing B cell epitopes on ricin toxin's enzymatic subunit. Proteins (2016)

Release Date

2016-07-20

Peptides

Ricin: A
VHH2(F5) antibody: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ricin

VHH2(F5) antibody

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