SMTL ID : 5u4l.1

RTA-V1C7_G29R-high-salt

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-mer

Ligands

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 7 residues within 4Å: Chain A: T.17, A.18, G.19, A.20, N.145 Chain B: S.61 Ligands: PO4.2 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:G.19, A:A.20, A:N.145, B:S.61, B:S.61, B:S.61 Water bridges: B:S.61, B:S.61 PO4.2: 8 residues within 4Å: Chain A: T.17, A.18, N.68, H.69, N.145, E.149 Ligands: PO4.1, EDO.9 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Water bridges: B:S.61, B:S.61, A:A.70 Hydrogen bonds: A:T.17, A:T.17, A:H.69, A:N.145 PO4.3: 4 residues within 4Å: Chain A: G.190, R.193, T.194, R.197 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.190 Salt bridges: A:R.193, A:R.197

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

CL.4: 3 residues within 4Å: Chain A: G.124, N.126, R.129 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: F.121, A.122 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: E.131, Q.132 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain A: T.120 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain A: R.129 Ligand excluded by PLIP

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

EDO.9: 6 residues within 4Å: Chain A: H.69 Chain B: D.36, Y.37, S.59, S.61 Ligands: PO4.2 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bazzoli, A. et al., Using homology modeling to interrogate binding affinity in neutralization of ricin toxin by a family of single domain antibodies. Proteins (2017)

Release Date

2017-12-13

Peptides

Ricin: A
V1C7 VHH antibody G29R variant: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ricin

V1C7 VHH antibody G29R variant