SMTL ID : 4lgr.1

Ricin A chain bound to camelid nanobody (VHH3)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

hetero-1-1-mer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: E.98, H.102 Ligands: ACY.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.98, A:E.98, A:H.102 ZN.11: 1 residues within 4Å: Chain B: H.120 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:H.120, H2O.7, H2O.7, H2O.7, H2O.7 ZN.12: 3 residues within 4Å: Chain B: H.20, D.78 Ligands: ACY.13 5 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: B:H.20, B:D.78, B:D.78, H2O.10, ACY.13

2 x ACY: ACETIC ACID(Non-functional Binders)

ACY.2: 3 residues within 4Å: Chain A: E.98, H.102 Ligands: ZN.1 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.101 Salt bridges: A:H.102 ACY.13: 4 residues within 4Å: Chain B: R.18, H.20, D.78 Ligands: ZN.12 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.18, B:H.20

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

CL.3: 1 residues within 4Å: Chain A: H.90 Ligand excluded by PLIP CL.4: 1 residues within 4Å: Chain A: R.189 Ligand excluded by PLIP CL.5: 1 residues within 4Å: Chain A: H.36 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: E.57, S.65, V.66, T.67 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: F.7, T.8 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain A: E.95 Ligand excluded by PLIP CL.14: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.15: 5 residues within 4Å: Chain B: V.4, E.5, S.6, H.20, A.22 Ligand excluded by PLIP

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

EDO.9: 5 residues within 4Å: Chain A: E.142, T.159, R.162, S.163, I.166 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.162 Water bridges: A:E.142, A:A.146 EDO.10: 5 residues within 4Å: Chain A: F.88, I.100, T.101, R.110, T.112 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.100, A:R.110

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rudolph, M.J. et al., Crystal Structures of Ricin Toxin's Enzymatic Subunit (RTA) in Complex with Neutralizing and Non-Neutralizing Single-Chain Antibodies. J.Mol.Biol. (2014)

Release Date

2014-06-11

Peptides

Ricin: A
Camelid nanobody (VHH3): B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ricin

Camelid nanobody (VHH3)

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