SMTL ID : 8fdd.1

Crystal structure of Ky15.3 Fab in complex with circumsporozoite protein NPDP peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: G.116, T.117, T.118 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.117, A:T.118, A:T.118 Water bridges: A:G.116 EDO.2: 3 residues within 4Å: Chain A: W.52 Chain C: A.6, N.7 No protein-ligand interaction detected (PLIP) EDO.3: 6 residues within 4Å: Chain A: L.151, V.179, S.187, L.188, S.189 Chain B: T.177 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:T.177, A:S.189 Water bridges: B:S.175, A:S.189, A:S.189 EDO.4: 5 residues within 4Å: Chain A: P.41, A.92, V.93, T.118, I.120 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.158 EDO.5: 4 residues within 4Å: Chain A: Y.60, G.61, E.62, K.65 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.62, A:K.65 Water bridges: B:Y.94 EDO.6: 7 residues within 4Å: Chain B: Q.37, K.45, P.59, R.61, F.62, D.81, D.82 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.37, B:R.61, B:D.81 EDO.7: 3 residues within 4Å: Chain B: A.111, P.112, S.113 2 PLIP interactions: 2 interactions with chain B Water bridges: B:P.112, B:V.114 EDO.8: 7 residues within 4Å: Chain B: L.11, S.12, A.13, D.17, R.18, V.19, K.106 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.17, B:D.17, B:K.106 Water bridges: B:R.18 EDO.9: 4 residues within 4Å: Chain B: V.109, A.110, A.111, G.199 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.111, B:G.199 EDO.10: 5 residues within 4Å: Chain B: Q.38, K.39, P.40, T.85, Y.87 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.85, B:Y.87, B:Y.87, A:Q.39 Water bridges: B:T.85 EDO.11: 3 residues within 4Å: Chain B: V.190, T.205, S.207 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.207 Water bridges: B:S.207, B:N.209

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

Ky15.3 Antibody, heavy chain: A
Ky15.3 Antibody, light chain: B
Circumsporozoite protein NPDP peptide: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
P

Ky15.3 Antibody, heavy chain

Ky15.3 Antibody, light chain

Circumsporozoite protein NPDP peptide

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