SMTL ID : 8da0.1 (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: 1 residues within 4Å: Chain A: C.214 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:C.214, H2O.1, H2O.5 ZN.2: 3 residues within 4Å: Chain A: E.213 Chain B: D.230, T.232 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Metal complexes: B:D.230, A:E.213, A:E.213 ZN.3: 2 residues within 4Å: Chain A: D.28 Ligands: ACT.9 4 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.28, H2O.5, H2O.5, ACT.9 ZN.4: 2 residues within 4Å: Chain A: K.183, E.187 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.187, A:E.187, H2O.5 ZN.5: 4 residues within 4Å: Chain A: N.137, N.138, S.174 Chain B: H.177 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.177, H2O.4, H2O.7 ZN.6: 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.7: 2 residues within 4Å: Chain A: N.210 Chain B: T.234 No protein-ligand interaction detected (PLIP) ZN.12: 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.9, H2O.10 ZN.13: 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.7, H2O.9, H2O.10

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

ACT.8: 4 residues within 4Å: Chain A: D.151, K.188, H.189 Ligands: ZN.6 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.189 ACT.9: 4 residues within 4Å: Chain A: D.28, S.67, G.68 Ligands: ZN.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.68 ACT.10: 3 residues within 4Å: Chain A: L.154, Q.155, S.156 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.156 ACT.11: 3 residues within 4Å: Chain A: P.59, R.61, E.81 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.61 ACT.15: 5 residues within 4Å: Chain B: R.38, Q.39, S.40, G.44, E.46 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.40, B:G.44, B:E.46 Salt bridges: B:R.38

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 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 A, 3 interactions with chain B Hydrogen bonds: A:S.162, A:T.178, B:F.179, B:S.190, B:S.192

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
A

B
B

C
E

Centi-LNX-D09 Fab light chain

Centi-LNX-D09 Fab heavy chain

Alpha-elapitoxin-Dpp2d

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