SMTL ID : 7c94.2 (1 other biounit)

Crystal structure of the anti-human podoplanin antibody Fab fragment complex with glycopeptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.84 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x A2G- GAL- SIA- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid-(2-6)]2-acetamido-2-deoxy-alpha-D-galactopyranose

A2G-GAL-SIA-SIA.1: 11 residues within 4Å: Chain A: N.31, Y.38, Y.98, S.99, T.100 Chain B: Y.57, T.58, Y.59, G.105, P.106 Chain C: T.10 8 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A, 1 interactions with chain C Hydrogen bonds: B:K.65, B:K.65, A:N.31, A:Y.98, A:S.99, A:S.99, A:T.100, C:T.10

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

PO4.2: 2 residues within 4Å: Chain A: S.71, G.72 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.72 PO4.3: 5 residues within 4Å: Chain A: Q.43, K.51, P.65, E.87, D.88 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.43, A:E.87 Salt bridges: A:K.45, A:K.51 PO4.7: 5 residues within 4Å: Chain B: Q.39, T.40, P.41, K.43, M.93 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:P.41, B:M.93 Salt bridges: B:K.43

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 2 residues within 4Å: Chain A: D.116, T.206 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.116, A:K.205 GOL.5: 3 residues within 4Å: Chain A: D.157, R.194, H.195 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.195 GOL.6: 11 residues within 4Å: Chain A: L.166, S.168, S.182, S.183, T.184 Chain B: F.175, P.176, V.178, T.185, L.186, S.187 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:P.176, B:S.187, B:S.187, A:S.168, A:S.182, A:T.184, A:T.184

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ogasawara, S. et al., Crystal structure of an anti-podoplanin antibody bound to a disialylated O-linked glycopeptide. Biochem.Biophys.Res.Commun. (2020)

Release Date

2020-09-30

Peptides

Light chain of Fab fragment: A
Heavy chain of Fab fragment: B
Peptide from Podoplanin: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

Light chain of Fab fragment

Heavy chain of Fab fragment

Peptide from Podoplanin

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