SMTL ID : 8da0.2 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-1-mer

Ligands

9 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: N.137, N.138 Chain B: H.177 Ligands: ACT.7 3 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: B:H.177, H2O.2, ACT.7 ZN.2: 1 residues within 4Å: Chain A: D.28 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.28, A:D.28, H2O.2, H2O.5, H2O.5 ZN.3: 3 residues within 4Å: Chain A: D.151, H.189 Ligands: ACT.8 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.151, A:H.189, ACT.8 ZN.4: 2 residues within 4Å: Chain A: K.183, E.187 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.187 ZN.5: 3 residues within 4Å: Chain A: E.213 Chain B: D.230, T.232 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Metal complexes: A:E.213, A:E.213, B:D.230 ZN.9: 2 residues within 4Å: Chain B: H.53 Ligands: ACT.13 3 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: B:H.53, H2O.7, ACT.13 ZN.10: 2 residues within 4Å: Chain B: E.72, D.79 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.79, H2O.6, H2O.6, H2O.7, H2O.8 ZN.11: 2 residues within 4Å: Chain B: D.52, H.58 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.52, B:H.58, H2O.8, H2O.9 ZN.12: 2 residues within 4Å: Chain A: N.210 Chain B: T.234 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.234, H2O.3, H2O.5, H2O.9

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 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 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:F.179, B:S.192, A:S.162, A:S.176, A:T.178

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

ACT.7: 7 residues within 4Å: Chain A: N.137, N.138, K.169 Chain B: G.175, H.177, T.196 Ligands: ZN.1 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.137, A:N.138 Salt bridges: A:K.169, B:H.177 ACT.8: 4 residues within 4Å: Chain A: D.151, K.188, H.189 Ligands: ZN.3 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.189 ACT.13: 3 residues within 4Å: Chain B: H.53, S.54 Ligands: ZN.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.54 Salt bridges: B:H.53 ACT.14: 3 residues within 4Å: Chain B: S.107, Y.108, Y.109 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.109

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
Alpha-elapitoxin-Dpp2d: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
F

Centi-LNX-D09 Fab light chain

Centi-LNX-D09 Fab heavy chain

Alpha-elapitoxin-Dpp2d

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