SMTL ID : 9clp.1

Structure of ecarin from the venom of Kenyan saw-scaled viper in complex with the Fab of neutralizing antibody H11

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

1 x UNK- UNK- UNK- UNK- UNK- UNK- UNK: Endogenous peptide

UNK-UNK-UNK-UNK-UNK-UNK-UNK.1: 11 residues within 4Å: Chain A: H.110, S.111, T.112, L.113, G.114, I.115, T.116, E.148, H.157, G.173, E.175 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.112, A:I.115 Hydrogen bonds: A:L.113, A:G.114, A:G.173

1 x ZN: ZINC ION

ZN.2: 3 residues within 4Å: Chain A: H.147, H.151, H.157 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.147, A:H.151, A:H.157, A:H.157

3 x CA: CALCIUM ION

CA.3: 6 residues within 4Å: Chain A: V.217, N.220, I.222, E.224, E.227, D.230 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:V.217, A:I.222, A:E.224, A:E.227, A:D.230 CA.4: 5 residues within 4Å: Chain A: R.274, D.281, V.282, N.296, E.297 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.281, A:V.282 CA.5: 4 residues within 4Å: Chain A: E.14, D.98, C.202, D.205 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.14, A:D.98, A:C.202

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Misson Mindrebo, L.E. et al., Importance of the Cysteine-Rich Domain of Snake Venom Prothrombin Activators: Insights Gained from Synthetic Neutralizing Antibodies. Toxins (2024)

Release Date

2024-09-11

Peptides

Zinc metalloproteinase-disintegrin-like ecarin: A
H11 Fab heavy chain: B
H11 Fab light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
L

Zinc metalloproteinase-disintegrin-like ecarin

H11 Fab heavy chain

H11 Fab light chain