SMTL ID : 7rth.3 (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

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

PO4.1: 7 residues within 4Å: Chain A: V.111, Y.141, P.142, Q.200 Chain C: K.146, T.198, P.205 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:K.146 PO4.2: 6 residues within 4Å: Chain A: V.116, F.117, I.118, K.208 Chain B: S.145, K.147 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.145, A:I.118 Salt bridges: B:K.147 PO4.3: 4 residues within 4Å: Chain A: S.122, D.123, S.124 Chain B: P.141 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Salt bridges: B:K.227 Hydrogen bonds: A:S.122, A:D.123, A:S.124 PO4.8: 4 residues within 4Å: Chain B: T.61, S.62, Y.63, K.68 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.62, B:Y.63, B:Y.63 Salt bridges: B:K.68 PO4.11: 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 PO4.12: 5 residues within 4Å: Chain C: P.114, S.115, V.116, V.206, K.208 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:P.114, C:V.116 Salt bridges: C:K.208 PO4.13: 5 residues within 4Å: Chain C: Q.161, T.179, T.181 Chain D: Q.189, S.195 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Q.161, C:T.179, C:T.179, C:T.181, D:Q.189, D:S.195 PO4.14: 4 residues within 4Å: Chain C: F.117, I.118, K.208 Chain D: S.145 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:I.118, D:S.145, D:S.145 Salt bridges: C:K.208 PO4.17: 5 residues within 4Å: Chain D: I.54, S.56, S.59, S.74, A.75 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:A.75 PO4.18: 4 residues within 4Å: Chain D: Y.60, Y.105, Q.107, Y.108 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.60, D:Q.107, D:Y.108 PO4.20: 4 residues within 4Å: Chain E: L.53, T.55, G.58, R.74 1 PLIP interactions: 1 interactions with chain E Salt bridges: E:R.74 PO4.21: 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 PO4.24: 6 residues within 4Å: Chain F: A.26, T.30, M.36, R.74, N.79, M.80 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:T.30 PO4.25: 3 residues within 4Å: Chain F: L.53, G.58, R.74 1 PLIP interactions: 1 interactions with chain F Salt bridges: F:R.74 PO4.26: 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

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

CL.4: 3 residues within 4Å: Chain A: P.60, S.61, R.62 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: Q.161 Chain B: V.187 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: W.106, W.114, G.116 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain C: Y.87, Y.88, C.89, G.102 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain D: W.106, W.114, G.116 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain B: N.31 Chain E: Q.113 Ligand excluded by PLIP CL.23: 3 residues within 4Å: Chain E: R.74, N.79, M.80 Ligand excluded by PLIP

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 8 residues within 4Å: Chain A: R.25, Y.87, Y.88, C.89, G.100, Q.101, G.102, T.103 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.25, A:R.25, A:C.89, A:Q.101, A:G.102, A:T.103, A:T.103 GOL.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.16: 6 residues within 4Å: Chain C: Q.38, K.46, L.48, P.60, F.63, D.83 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.38, C:D.83

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

PEG.10: 4 residues within 4Å: Chain B: Y.60, Y.105, Q.107, Y.108 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.108

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
G

C
I

B
H

D
J

E
g

F
i

Fragment Antigen-Binding Light Chain

Fragment Antigen-Binding Heavy Chain

Nanobody

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