SMTL ID : 7rth.1 (4 other biounits)

Crystal structure of an anti-lysozyme nanobody in complex with an anti-nanobody Fab "NabFab

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.19 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

PO4.1: 4 residues within 4Å: Chain B: Y.60, Y.105, Q.107, Y.108 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain B Salt bridges: C:K.121 Hydrogen bonds: B:Q.107, B:Q.107, B:Y.108 PO4.5: 3 residues within 4Å: Chain C: T.55, G.58, R.74 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.55, C:T.55 Salt bridges: C:R.74 PO4.6: 3 residues within 4Å: Chain C: P.106, V.107, R.108 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.107, C:R.108 Salt bridges: C:R.108

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

CL.2: 2 residues within 4Å: Chain B: N.31 Chain C: Q.113 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain B: W.106, W.114, G.116 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain B: G.29, F.30, N.80 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bloch, J.S. et al., Development of a universal nanobody-binding Fab module for fiducial-assisted cryo-EM studies of membrane proteins. Proc.Natl.Acad.Sci.USA (2021)

Release Date

2021-09-01

Peptides

Fragment Antigen-Binding Light Chain: A
Fragment Antigen-Binding Heavy Chain: B
Nanobody: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
a

Fragment Antigen-Binding Light Chain

Fragment Antigen-Binding Heavy Chain

Nanobody

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