SMTL ID : 6o2c.1

Crystal structure of 4493 Fab in complex with circumsporozoite protein NANP3 and anti-kappa VHH domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.02 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: K.152, Q.180, S.181, S.182 Chain B: T.181 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.152, A:K.152, A:S.181, A:S.181, A:S.182 Water bridges: A:S.182 EDO.2: 3 residues within 4Å: Chain A: V.95, Q.114, G.115 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.114 EDO.3: 6 residues within 4Å: Chain A: L.150, V.178, S.186, L.187, S.188 Chain B: T.179 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.186, A:S.188, B:T.179 Water bridges: A:S.188, A:S.188, B:S.177, B:S.177 EDO.5: 3 residues within 4Å: Chain B: S.30, T.32, Y.33 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.30, B:S.30, B:T.32 EDO.6: 6 residues within 4Å: Chain B: S.64, G.65, S.66, T.73, L.74, T.75 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.66, B:T.73, B:T.75 Water bridges: B:S.64, B:S.64, B:G.65 EDO.7: 3 residues within 4Å: Chain B: A.113, P.114, S.115 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:P.114 Water bridges: B:A.113, B:S.115

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

PGE.4: 8 residues within 4Å: Chain A: G.42, K.43 Chain B: G.9, T.10, Y.88, Q.101, G.102, K.104 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.42, B:Y.88 Water bridges: A:Q.39, A:K.43

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 4 residues within 4Å: Chain C: Q.3, X.5, X.23, X.25 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Murugan, R. et al., Evolution of protective human antibodies against Plasmodium falciparum circumsporozoite protein repeat motifs. Nat. Med. (2020)

Release Date

2020-07-01

Peptides

4493 Fab heavy chain: A
4493 Kappa light chain: B
Anti-kappa VHH domain: C
Circumsporozoite protein: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
K

D
C

4493 Fab heavy chain

4493 Kappa light chain

Anti-kappa VHH domain

Circumsporozoite protein

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