SMTL ID : 9f1i.1 (1 other biounit)

Crystal structure of a first-in-class antibody for alpha-1,6-fucosylated prostate-specific antigen, target bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.38 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-FUC.1: 12 residues within 4Å: Chain A: A.30, G.31, Y.32, D.33, Y.52, A.53, D.54, D.105, Y.106 Chain C: N.3, K.4, I.7 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:Y.52, C:K.4 Hydrogen bonds: A:G.31, A:Y.32, A:Y.32, A:D.33, A:A.53, A:D.54, A:D.54, A:D.54, A:D.105, A:D.54 Water bridges: A:G.107, C:N.3, A:S.58

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 9 residues within 4Å: Chain A: F.177, P.178, V.180, S.188, L.189, S.190 Chain B: S.167, S.181, T.183 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:P.178, A:S.190, B:S.167, B:S.181 EDO.3: 3 residues within 4Å: Chain B: N.31, Y.32, K.50 2 PLIP interactions: 2 interactions with chain B Water bridges: B:N.31, B:N.31 EDO.4: 4 residues within 4Å: Chain B: Q.160, L.186, Q.190, H.194 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.160 Water bridges: B:T.158, B:T.158, B:Q.160 EDO.5: 5 residues within 4Å: Chain B: Q.37, K.45, L.47, P.59, F.62 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.37, B:Q.37

1 x PFX: 2-[2-(2-azanylethoxy)ethoxy]ethanoic acid(Non-covalent)

PFX.6: 8 residues within 4Å: Chain A: Y.52, S.58, T.59, Y.60 Chain C: I.1, R.2, N.3, K.4 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:I.1, C:N.3, C:K.4, A:Y.52 Water bridges: C:R.2, C:R.2, C:R.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Halldorsson, S. et al., Development of a first-in-class antibody and a specific assay for alpha-1,6-fucosylated prostate-specific antigen. Sci Rep (2024)

Release Date

2024-07-31

Peptides

Heavy chain rabbit fab: A
Light chain rabbit fab: B
Prostate specific antigen: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
P

Heavy chain rabbit fab

Light chain rabbit fab

Prostate specific antigen

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