SMTL ID : 7c95.1 (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

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: K.155, T.199, E.201, V.212 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.155, A:T.199 Water bridges: A:G.158 GOL.2: 4 residues within 4Å: Chain A: G.134, T.188, K.189, D.190 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.134, A:K.189, A:K.189, A:K.189, A:D.190 GOL.3: 2 residues within 4Å: Chain A: A.117, A.118 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.118 GOL.7: 5 residues within 4Å: Chain B: G.9, G.10, T.116, L.117, P.158 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.116, B:L.117 GOL.8: 7 residues within 4Å: Chain B: E.157, V.159, T.174, F.175, P.176, A.177, L.186 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.159, B:A.177

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

SO4.4: 4 residues within 4Å: Chain A: R.161, L.187, T.188, E.191 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.188, A:T.188 Water bridges: A:R.161 Salt bridges: A:R.161 SO4.5: 4 residues within 4Å: Chain A: Q.43, K.45, Q.48, K.51 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.43, A:Q.48 Water bridges: A:K.45 Salt bridges: A:K.45 SO4.9: 5 residues within 4Å: Chain B: S.52, N.53, G.54, G.55, S.56 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

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.6: 9 residues within 4Å: Chain A: Q.44, K.45, P.46, G.47, Q.48, D.171 Chain B: Q.39, M.93, Y.95 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Water bridges: B:Y.95 Hydrogen bonds: A:G.47, A:Q.48, A:D.171

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
C

B
D

Light chain of Fab fragment

Heavy chain of Fab fragment

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