SMTL ID : 9fyt.1

mAbs in complex with cobratoxin at pH 4.5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

hetero-2-2-2-mer

Ligands

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 3 residues within 4Å: Chain A: V.48, K.49, V.52 Ligand excluded by PLIP CL.2: 5 residues within 4Å: Chain A: R.70 Chain E: Y.114, Y.115 Chain F: W.93, S.95 Ligand excluded by PLIP CL.3: 4 residues within 4Å: Chain A: R.70, P.71 Chain B: P.71 Chain E: D.113 Ligand excluded by PLIP

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain B: I.1, G.17, H.18, D.60 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.1, B:H.18 GOL.5: 4 residues within 4Å: Chain B: R.2, S.11, K.12, D.13 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.13 Water bridges: B:S.11 GOL.7: 7 residues within 4Å: Chain D: Q.39, K.41, V.47, V.49, I.60, P.61, F.64 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Q.39 Water bridges: D:Q.39, D:K.41, D:K.41, D:R.63 GOL.9: 7 residues within 4Å: Chain F: Q.39, K.41, V.47, V.49, I.60, P.61, F.64 4 PLIP interactions: 4 interactions with chain F Water bridges: F:Q.39, F:K.41, F:K.41, F:R.63 GOL.10: 10 residues within 4Å: Chain E: G.43, Q.44, G.45 Chain F: P.11, D.87, Y.89, G.104, G.105, T.106, K.107 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:D.87, F:G.105, F:K.107 Water bridges: E:G.43

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

SO4.6: 5 residues within 4Å: Chain C: E.11, K.13, S.18, V.19, K.20 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:K.20, C:K.20 Water bridges: C:K.13, C:K.13, C:S.18 Salt bridges: C:K.13

2 x NA: SODIUM ION(Non-functional Binders)

NA.8: 4 residues within 4Å: Chain D: R.63, S.65, T.76, S.78 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.76, D:S.78 NA.11: 4 residues within 4Å: Chain F: R.63, S.65, T.76, S.78 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:R.63, F:S.78, F:S.78

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

wade, J., Structural mechanisms of a-neurotoxin-neutralizing antibodies enable rational design of pH-dependent antigen binding. To Be Published

Release Date

2025-07-16

Peptides

Alpha-cobratoxin: AB
Light chain scFv A01: CE
heavy chain scFv Ao1: DF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
I

E
C

D
M

F
D

Alpha-cobratoxin

Light chain scFv A01

heavy chain scFv Ao1

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