SMTL ID : 8fa8.1

Crystal structure of Ky15.11 Fab in complex with circumsporozoite protein NDN peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: T.61, D.62 Chain B: D.1, Y.94 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.61, A:D.62, B:D.1 EDO.2: 3 residues within 4Å: Chain A: H.180 Chain B: T.163, E.164 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:H.180, B:E.164 Water bridges: A:T.181, B:T.163 EDO.3: 5 residues within 4Å: Chain A: S.143, K.145 Chain B: I.116, S.207, F.208 2 PLIP interactions: 2 interactions with chain B Water bridges: B:S.207, B:S.207 EDO.4: 7 residues within 4Å: Chain B: Q.37, K.45, L.47, I.58, P.59, F.62, D.81 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.37, B:K.45, B:D.81 Water bridges: B:Q.37, B:R.61 EDO.5: 8 residues within 4Å: Chain A: K.230 Chain B: P.118, Y.185, F.208, N.209, R.210, G.211, E.212 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.185, B:Y.185, B:G.211, B:E.212, A:K.230 Water bridges: B:N.209, B:N.209 EDO.6: 5 residues within 4Å: Chain A: T.112, S.113 Chain B: W.32, S.92 Chain C: N.1 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.92, A:T.112 EDO.7: 5 residues within 4Å: Chain B: V.149, Q.154, L.180, D.184, H.188 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.154 Water bridges: B:D.184 EDO.8: 3 residues within 4Å: Chain A: Y.59 Chain B: Y.94 Chain C: N.1 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Water bridges: C:N.1, C:N.1, C:A.2 Hydrogen bonds: A:Y.59, A:Y.59

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

Ky15.11 Antibody, heavy chain: A
Ky15.11 Antibody, light chain: B
Circumsporozoite protein NDN peptide: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
P

Ky15.11 Antibody, heavy chain

Ky15.11 Antibody, light chain

Circumsporozoite protein NDN peptide

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