SMTL ID : 7rth.2 (4 other biounits)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.19 Å

Oligo State

hetero-2-2-2-mer

Ligands

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

PO4.1: 6 residues within 4Å: Chain A: S.115, F.117, N.138, N.139 Chain B: T.153, T.201 Ligand excluded by PLIP PO4.2: 3 residues within 4Å: Chain A: P.60, S.61, R.62 Ligand excluded by PLIP PO4.3: 4 residues within 4Å: Chain A: Q.38, L.48, V.59, P.60 Ligand excluded by PLIP PO4.4: 5 residues within 4Å: Chain A: V.116, F.117, I.118, K.208 Chain B: S.145 Ligand excluded by PLIP PO4.5: 5 residues within 4Å: Chain A: P.114, S.115, V.116, V.206, K.208 Ligand excluded by PLIP PO4.9: 6 residues within 4Å: Chain B: Y.53, Y.60, Y.105, Q.107, Y.108 Chain E: K.121 Ligand excluded by PLIP PO4.10: 4 residues within 4Å: Chain B: I.54, S.56, S.74, A.75 Ligand excluded by PLIP PO4.13: 4 residues within 4Å: Chain C: F.117, I.118, K.208 Chain D: S.145 Ligand excluded by PLIP PO4.14: 3 residues within 4Å: Chain C: P.60, S.61, R.62 Ligand excluded by PLIP PO4.15: 5 residues within 4Å: Chain C: S.115, F.117, N.138, N.139 Chain D: T.201 Ligand excluded by PLIP PO4.16: 5 residues within 4Å: Chain C: S.122, D.123, S.124 Chain D: P.141, K.232 Ligand excluded by PLIP PO4.22: 3 residues within 4Å: Chain E: P.106, V.107, R.108 Ligand excluded by PLIP PO4.23: 5 residues within 4Å: Chain E: L.53, Y.54, T.55, G.58, R.74 Ligand excluded by PLIP PO4.25: 4 residues within 4Å: Chain F: T.55, T.57, G.58, R.74 Ligand excluded by PLIP PO4.26: 2 residues within 4Å: Chain F: V.107, R.108 Ligand excluded by PLIP PO4.27: 7 residues within 4Å: Chain F: A.26, T.30, M.36, R.74, N.79, M.80, V.81 Ligand excluded by PLIP

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

CL.6: 4 residues within 4Å: Chain A: Y.87, C.89, G.102, T.103 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: V.111, Q.200 Chain C: P.205 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain B: N.31 Chain E: Q.113 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain B: W.106, W.114, G.116 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain C: Q.161 Chain D: V.187 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain C: Y.87, Y.88, C.89, G.102 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain D: W.106, W.114, G.116 Ligand excluded by PLIP CL.28: 1 residues within 4Å: Chain F: D.31 Ligand excluded by PLIP

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 7 residues within 4Å: Chain A: Q.161, T.179, T.181 Chain B: K.161, V.187, Q.189, S.195 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.195, B:S.195 GOL.19: 6 residues within 4Å: Chain A: T.198, S.203, P.205 Chain C: V.111, P.142, Q.200 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:T.198, A:T.198, A:S.203, C:Q.200 GOL.24: 3 residues within 4Å: Chain E: Y.104, V.105, P.106 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Y.104

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

PEG.21: 5 residues within 4Å: Chain D: Y.60, Y.105, Q.107, Y.108 Chain F: K.121 No protein-ligand interaction detected (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
C

C
E

B
D

D
F

E
c

F
e

Fragment Antigen-Binding Light Chain

Fragment Antigen-Binding Heavy Chain

Nanobody

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