SMTL ID : 7rth.4 (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: 4 residues within 4Å: Chain A: G.129, S.183, K.184, A.185 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.129, A:K.184, A:A.185 PO4.2: 7 residues within 4Å: Chain A: T.198, L.202, S.203, S.204, P.205 Chain C: V.111, Q.200 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Q.200, A:S.203 PO4.5: 7 residues within 4Å: Chain A: Q.161, T.179, T.181 Chain B: K.161, V.187, Q.189, S.195 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.195, A:T.179, A:T.181 Salt bridges: B:K.161 PO4.8: 3 residues within 4Å: Chain C: S.115, N.138 Chain D: T.201 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:T.201, C:S.115, C:S.115, C:S.115 PO4.9: 3 residues within 4Å: Chain C: P.60, S.61, R.62 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.61, C:S.61, C:R.62 Salt bridges: C:R.62 PO4.10: 6 residues within 4Å: Chain C: Q.161, T.179, T.181 Chain D: V.187, Q.189, S.195 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:S.195, C:Q.161, C:T.179 PO4.16: 5 residues within 4Å: Chain F: L.53, Y.54, T.55, G.58, R.74 1 PLIP interactions: 1 interactions with chain F Salt bridges: F:R.74 PO4.17: 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: S.115, N.138 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: C.89, Q.101, G.102 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain B: F.30, N.31 Ligand excluded by PLIP CL.11: 1 residues within 4Å: Chain C: V.116 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain D: N.31, Y.35 Chain F: E.46 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain C: V.30 Chain D: A.110 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 5 residues within 4Å: Chain B: Y.60, Y.105, Q.107, Y.108 Chain E: K.121 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.107 GOL.15: 3 residues within 4Å: Chain E: L.53, T.55, R.74 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:T.55, E:R.74

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.14: 4 residues within 4Å: Chain D: Y.60, Y.105, Q.107, Y.108 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.107, D:Q.107, D:Y.108 Water bridges: D:Y.53

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
K

C
M

B
L

D
N

E
k

F
m

Fragment Antigen-Binding Light Chain

Fragment Antigen-Binding Heavy Chain

Nanobody

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