SMTL ID : 9f1i.2 (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(Post Translational Modification)

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 Hydrogen bonds: A:G.31, A:Y.32, A:Y.32, A:A.53, A:D.54, A:D.54, A:D.105, A:Y.52 Water bridges: A:G.107, C:N.3, A:S.58 Hydrophobic interactions: C:K.4

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

EDO.2: 3 residues within 4Å: Chain A: R.38, E.46, W.64 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.38, A:E.46 EDO.3: 6 residues within 4Å: Chain B: V.155, T.158, Q.160, L.186, Q.190, H.194 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.160, B:Q.190

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

PFX.4: 8 residues within 4Å: Chain A: Y.52, S.58, T.59 Chain B: D.98 Chain C: I.1, R.2, N.3, K.4 9 PLIP interactions: 1 interactions with chain B, 8 interactions with chain C Hydrogen bonds: B:D.98, C:N.3, C:K.4 Water bridges: C:I.1, C:I.1, C:I.1, C:I.1, 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
I

B
M

C
Q

Heavy chain rabbit fab

Light chain rabbit fab

Prostate specific antigen

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