SMTL ID : 6o23.1

Crystal structure of 2243 Fab in complex with circumsporozoite protein NANP5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-2-2-1-mer

Ligands

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

EDO.1: 2 residues within 4Å: Chain A: R.16, S.17 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.17 EDO.2: 4 residues within 4Å: Chain A: E.46, A.61, D.62, S.63 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.63, A:S.63 Water bridges: A:W.47, A:D.62 EDO.3: 8 residues within 4Å: Chain A: W.52, N.57, Y.59 Chain C: Y.53 Chain E: N.9, A.10, N.11 Ligands: SO4.24 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:N.9, E:N.11, A:N.57, A:Y.59 EDO.4: 6 residues within 4Å: Chain A: L.200, G.201, T.202, Q.203, T.204, R.221 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.204, A:R.221 EDO.8: 4 residues within 4Å: Chain A: P.134 Chain B: S.120, D.121, E.122 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.121, B:E.122, B:E.122, B:E.122 EDO.9: 4 residues within 4Å: Chain B: K.189, N.209, R.210, G.211 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.189, B:N.209, B:R.210 EDO.11: 6 residues within 4Å: Chain B: S.93 Chain C: D.101, A.103 Chain E: N.11, P.12, N.13 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.11 EDO.12: 7 residues within 4Å: Chain C: L.100, D.101, D.102, S.105, C.108 Chain E: N.7, N.9 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain C Hydrogen bonds: E:N.7, E:N.9, C:D.102 Water bridges: E:N.7, E:N.9, C:L.100 EDO.13: 6 residues within 4Å: Chain C: L.152, V.180, S.188, L.189, S.190 Chain D: T.177 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:S.190, D:T.177 Water bridges: C:S.190, C:S.190, D:Q.159, D:S.175 EDO.16: 8 residues within 4Å: Chain D: Q.37, K.45, P.59, R.61, F.62, D.81, D.82 Ligands: SO4.19 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Q.37, D:K.45, D:K.45, D:R.61, D:D.81 EDO.17: 2 residues within 4Å: Chain D: S.155, G.156 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.155, D:G.156 Water bridges: D:Q.154, D:S.158, D:S.158 EDO.18: 3 residues within 4Å: Chain D: D.104, I.105, Q.165 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:I.105, D:Q.165 Water bridges: D:K.102, D:K.102, D:Q.165, D:Y.172 EDO.23: 6 residues within 4Å: Chain A: S.31, Y.32, D.101 Chain E: N.17, A.18, N.19 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:A.18, E:N.19, E:N.19, E:N.19 Water bridges: A:S.31

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

SO4.5: 5 residues within 4Å: Chain A: S.141, T.142, S.143, S.197, S.198 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.141, A:T.142, A:S.143, A:S.197 SO4.6: 2 residues within 4Å: Chain A: S.25, G.26 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.26 SO4.7: 3 residues within 4Å: Chain A: F.27, T.28, Y.32 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.28 Water bridges: A:T.28, A:Y.32, A:Y.32 SO4.10: 3 residues within 4Å: Chain B: P.59, R.61, D.81 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.61 SO4.14: 3 residues within 4Å: Chain C: N.166, A.169, Q.203 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.166, C:Q.203 SO4.19: 4 residues within 4Å: Chain D: P.59, R.61, D.81 Ligands: EDO.16 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.81 Salt bridges: D:R.61 SO4.20: 3 residues within 4Å: Chain D: R.141, V.162, E.164 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Water bridges: D:V.162, D:V.162, C:G.42 Salt bridges: D:K.102, D:R.141 SO4.21: 1 residues within 4Å: Chain D: D.1 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.1 SO4.22: 4 residues within 4Å: Chain D: S.67, G.68, T.69, E.70 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.67, D:T.69, D:E.70 SO4.24: 4 residues within 4Å: Chain E: N.7, N.11, A.14 Ligands: EDO.3 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:N.7, E:N.11 Water bridges: E:N.7, E:N.7

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.15: 4 residues within 4Å: Chain D: P.8, S.9, T.10, E.142 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.9, D:S.9, D:T.10, D:T.10 Water bridges: D:T.10

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

2020-03-04

Peptides

2243 Fab heavy chain: AC
2243 kappa light chain: BD
Circumsporozoite protein: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
E

2243 Fab heavy chain

2243 kappa light chain

Circumsporozoite protein

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