SMTL ID : 8t8i.1

Structure of VHH-Fab complex with engineered Elbow FNQIKG, Crystal Kappa and SER substitutions

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.52 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x SIN: SUCCINIC ACID(Non-covalent)

SIN.1: 1 residues within 4Å: Chain A: Y.104 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.54

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

PEG.2: 2 residues within 4Å: Chain A: L.13, Q.15 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.15

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

PO4.3: 5 residues within 4Å: Chain B: P.114, S.115, V.116, V.204, K.206 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.116, B:V.116 Salt bridges: B:K.206 PO4.4: 5 residues within 4Å: Chain B: A.113, P.114, S.115, N.138, N.139 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.113, B:S.115, B:S.115, B:S.115 Water bridges: B:N.138

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

CL.5: 5 residues within 4Å: Chain B: Q.4, T.98, F.99 Chain C: E.49, W.50 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain A: Y.97 Chain C: Y.103, Q.104, Y.105, H.109 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bruce, H.A. et al., Engineered antigen-binding fragments for enhanced crystallization of antibody:antigen complexes. Protein Sci. (2024)

Release Date

2023-11-29

Peptides

VHH domain: A
Fab light chain: B
Fab heavy chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
L

C
H

VHH domain

Fab light chain

Fab heavy chain

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