SMTL ID : 8d9z.1

Crystal structure of Cobra alpha-neurotoxin in complex with Centi-LNX-D09 antibody

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-1-mer

Ligands

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: Q.37, K.45, P.59, R.61, F.62, E.81, D.82 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.37, A:K.45, A:E.81 Water bridges: A:K.39 GOL.2: 7 residues within 4Å: Chain A: L.4, F.98, G.99, Q.100 Chain B: K.43, G.44, L.45 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:L.4, B:K.43, B:L.45, B:L.45 GOL.3: 4 residues within 4Å: Chain A: S.67, G.68, T.69, D.70 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.67, A:T.69, A:T.69, A:D.70, A:D.70 Water bridges: A:S.67 GOL.4: 5 residues within 4Å: Chain A: S.121, D.122, E.123 Chain B: P.136, K.222 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.122, A:E.123, A:E.123, A:E.123, B:K.222 Water bridges: A:P.120 GOL.5: 4 residues within 4Å: Chain A: T.129, T.180, L.181, S.182 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.180 GOL.6: 6 residues within 4Å: Chain B: Y.59, K.64, G.65, R.66, F.67, T.68 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.65, B:T.68 GOL.7: 11 residues within 4Å: Chain A: Q.160, S.162, S.176, S.177, T.178 Chain B: F.179, P.180, V.182, S.190, L.191, S.192 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.162, A:S.177, A:T.178, B:F.179, B:S.190, B:S.192 GOL.8: 4 residues within 4Å: Chain B: S.105, G.106, S.107, Y.108 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.107 Water bridges: B:S.105 GOL.9: 7 residues within 4Å: Chain B: F.32, R.97, T.99, L.100, Y.101, D.114 Chain C: P.7 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:R.97, B:L.100, B:L.100 Water bridges: B:Y.101, B:D.114, C:R.36, C:R.36 GOL.10: 8 residues within 4Å: Chain B: G.10, F.11, L.121, V.122, T.123, P.160, E.161, P.215 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.121, B:T.123, B:T.123

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.11: 2 residues within 4Å: Chain C: K.23, V.52 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Water bridges: A:S.56 Hydrophobic interactions: C:V.52 Salt bridges: C:K.23

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Glanville, J. et al., Venom protection by antibody from a snakebite hyperimmune subject. To Be Published

Release Date

2023-06-14

Peptides

Centi-LNX-D09 Fab light chain: A
Centi-LNX-D09 Fab heavy chain: B
Long neurotoxin 1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

Centi-LNX-D09 Fab light chain

Centi-LNX-D09 Fab heavy chain

Long neurotoxin 1

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