SMTL ID : 3eyv.1

Anti-Lewis Y Fab fragment with Lewis Y antigen in the presence of zinc ions

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-2-2-mer

Ligands

1 x NDG- GAL- FUC- FUC: alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-alpha-D-glucopyranose

NDG-GAL-FUC-FUC.1: 13 residues within 4Å: Chain A: H.31, N.33, Y.37, F.101 Chain B: D.31, Y.32, Y.33, Y.35, T.100, R.101, G.103, S.104, W.105 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.105, A:Y.37, B:Y.32, B:R.101 Hydrogen bonds: B:T.100, B:S.104, B:Y.35, B:W.105, A:H.31, B:Y.33 Water bridges: B:Y.33, B:G.99

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: N.142, N.143 Chain B: H.170 Chain D: E.1 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Metal complexes: D:E.1, B:H.170 ZN.3: 2 residues within 4Å: Chain A: D.190, H.194 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.190, A:H.194 ZN.4: 4 residues within 4Å: Chain B: E.1 Chain C: N.142, N.143 Chain D: H.170 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: B:E.1, B:E.1, D:H.170, H2O.2 ZN.5: 2 residues within 4Å: Chain C: D.190, H.194 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.194

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 0 residues within 4Å: (No contacts) 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.100 Water bridges: D:Y.35, D:Y.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Farrugia, W. et al., A possible role for metallic ions in the carbohydrate cluster recognition displayed by a lewis y specific antibody. Plos One (2009)

Release Date

2009-11-03

Peptides

hu3S193 Fab, light chain: AC
hu3S193 Fab, heavy chain: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

C
A

B
H

D
B

hu3S193 Fab, light chain

hu3S193 Fab, heavy chain

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