SMTL ID : 7c95.2 (1 other biounit)

Crystal structure of the anti-human podoplanin antibody Fab fragment

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.13 Å

Oligo State

hetero-1-1-mer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: Q.48, S.49 Chain B: W.112, G.113, Q.114 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:W.112, A:S.49, A:S.49 GOL.2: 3 residues within 4Å: Chain A: T.206, S.207, T.208 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.207, A:S.207, A:T.208 GOL.3: 4 residues within 4Å: Chain A: E.160, R.161, Q.162, N.163 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.161, A:Q.162, A:N.163, A:N.163

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 2 residues within 4Å: Chain A: S.32, Y.98 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.32, A:S.32, A:Y.98 SO4.5: 4 residues within 4Å: Chain A: P.46, G.47, D.171 Chain B: K.43 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.47, A:D.171 Salt bridges: B:K.43 SO4.6: 3 residues within 4Å: Chain A: K.45, Q.48, K.51 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.45, A:K.51 SO4.7: 4 residues within 4Å: Chain A: T.188, D.190, E.191, R.194 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.188, A:T.188 Salt bridges: A:R.194 SO4.8: 3 residues within 4Å: Chain B: F.27, T.28, Y.32 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.28 SO4.9: 6 residues within 4Å: Chain B: S.52, N.53, G.54, G.55, S.56, Y.57 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.52, B:S.52, B:G.54, B:G.55, B:S.56

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Light chain of Fab fragment

Heavy chain of Fab fragment

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