SMTL ID : 7kbk.1

Ricin bound to VHH antibody V6E11

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- FUC: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-FUC.1: 3 residues within 4Å: Chain A: I.8, N.10 Ligands: EDO.5 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.31, A:R.31

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.2: 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-BMA.3: 9 residues within 4Å: Chain A: F.226, A.227, P.229, Y.243 Chain B: I.10, V.11, T.43, L.48, N.135 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:A.227 Hydrophobic interactions: B:I.10

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 5 residues within 4Å: Chain A: A.118, F.119, G.120, N.122, R.125 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.120, A:N.122 Water bridges: A:G.121, A:N.122

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

EDO.5: 5 residues within 4Å: Chain A: I.9, N.10, F.24, A.27 Ligands: NAG-NAG-BMA-FUC.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.10, A:N.10 Water bridges: A:F.24 EDO.8: 8 residues within 4Å: Chain B: D.22, V.23, R.24, D.25, G.26, Q.35, W.37, N.46 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.22, B:D.25, B:D.25, B:G.26, B:Q.35, B:N.46 Water bridges: B:K.40 EDO.9: 8 residues within 4Å: Chain B: D.234, V.235, R.236, A.237, I.246, Y.248, H.251, N.255 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.237, B:H.251, B:N.255

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

CL.6: 3 residues within 4Å: Chain A: Y.115, F.117, A.118 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: N.132, L.133, N.136 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain B: Y.69, A.84, R.102 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain B: R.27, F.28 Ligand excluded by PLIP CL.12: 1 residues within 4Å: Chain B: S.114 Ligand excluded by PLIP CL.13: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.14: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rudolph, M.J. et al., Structural Analysis of Toxin-Neutralizing, Single-Domain Antibodies that Bridge Ricin's A-B Subunit Interface. J.Mol.Biol. (2021)

Release Date

2021-08-04

Peptides

Ricin: A
Ricin: B
VHH antibody V6E11: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Ricin

Ricin

VHH antibody V6E11

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