SMTL ID : 7rth.5 (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-2-2-2-mer

Ligands

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

PO4.1: 5 residues within 4Å: Chain A: P.114, S.115, V.116, V.206, K.208 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.116 Salt bridges: A:K.208 PO4.2: 4 residues within 4Å: Chain A: V.116, F.117, I.118, K.208 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.118 PO4.4: 3 residues within 4Å: Chain C: K.108, R.109, T.110 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.108 PO4.5: 3 residues within 4Å: Chain D: N.173, A.176, Q.210 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.173, D:Q.210 PO4.9: 6 residues within 4Å: Chain E: T.30, M.36, T.55, R.74, K.76, N.79 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:T.30, E:N.79 Salt bridges: E:R.74 PO4.10: 6 residues within 4Å: Chain B: F.30, N.31, Y.35 Chain E: E.46, R.47, Q.113 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain E Hydrogen bonds: B:N.31, E:R.47, E:Q.113 PO4.11: 3 residues within 4Å: Chain E: P.106, V.107, R.108 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:V.107, E:R.108 Salt bridges: E:R.108 PO4.12: 3 residues within 4Å: Chain F: P.106, V.107, R.108 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:V.107, F:R.108 Salt bridges: F:R.108

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

CL.3: 2 residues within 4Å: Chain A: Q.161 Chain B: Q.189 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain D: Q.107, Y.108 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain D: W.106, W.114, G.116 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain D: Q.189 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain F: R.74, N.79 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain D: N.31 Chain F: E.46, Q.113 Ligand excluded by PLIP

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: AC
Fragment Antigen-Binding Heavy Chain: BD
Nanobody: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
O

C
Q

B
P

D
R

E
o

F
q

Fragment Antigen-Binding Light Chain

Fragment Antigen-Binding Heavy Chain

Nanobody

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