SMTL ID : 8f9u.1

Crystal structure of Ky15.7 Fab in complex with circumsporozoite protein NPDP peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

EDO.1: 3 residues within 4Å: Chain B: F.27, T.28, R.32 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.28, B:T.28, B:R.32 Water bridges: B:T.28 EDO.2: 5 residues within 4Å: Chain B: Q.39, T.40, P.41, G.44 Chain C: Y.87 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Water bridges: C:Y.87, C:Y.87, B:P.41 Hydrogen bonds: B:Q.39 EDO.3: 3 residues within 4Å: Chain B: V.161, S.162 Chain C: K.42 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:K.42, B:V.161 EDO.4: 6 residues within 4Å: Chain B: L.150, V.178, S.186, L.187, S.188 Chain C: T.177 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain B Water bridges: C:S.175, C:T.177, C:T.177, B:S.188, B:S.188 Hydrogen bonds: B:S.188 EDO.5: 2 residues within 4Å: Chain B: K.215, D.217 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.215, B:K.215 Water bridges: B:V.216 EDO.6: 5 residues within 4Å: Chain B: Y.60, A.61, D.62 Chain C: D.1, Y.94 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.62 Water bridges: B:S.63 EDO.7: 6 residues within 4Å: Chain B: V.172, H.173 Chain C: T.163, E.164, D.166 Ligands: EDO.8 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:H.173, C:D.166 Water bridges: B:T.174, B:T.174, C:T.163, C:T.163, C:E.164 EDO.8: 6 residues within 4Å: Chain C: F.83, E.164, Q.165, D.166, S.167 Ligands: EDO.7 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.166, C:S.167 Water bridges: C:K.39, C:F.83, C:S.167 EDO.9: 3 residues within 4Å: Chain B: P.176 Chain C: P.40, E.164 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:E.164 Water bridges: B:T.174 EDO.10: 3 residues within 4Å: Chain C: R.141, V.162, L.174 2 PLIP interactions: 2 interactions with chain C Water bridges: C:R.141, C:A.143

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thai, E. et al., Molecular determinants of cross-reactivity and potency by VH3-33 antibodies against the Plasmodium falciparum circumsporozoite protein. Cell Rep (2023)

Release Date

2023-11-01

Peptides

Circumsporozoite protein NPDP peptide: A
Ky15.7 Antibody, heavy chain: B
Ky15.7 Antibody, light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
P

B
A

C
B

Circumsporozoite protein NPDP peptide

Ky15.7 Antibody, heavy chain

Ky15.7 Antibody, light chain

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