SMTL ID : 6vvu.1

Anti-Tryptase fab E104.v1 bound to tryptase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-4-4-4-mer

Ligands

3 x CA: CALCIUM ION(Non-covalent)

CA.1: 3 residues within 4Å: Chain A: N.165, D.166 Ligands: 0GJ.2 No protein-ligand interaction detected (PLIP) CA.3: 3 residues within 4Å: Chain B: N.165, D.166 Ligands: 0GJ.4 No protein-ligand interaction detected (PLIP) CA.5: 3 residues within 4Å: Chain C: N.165, D.166 Ligands: 0GJ.6 No protein-ligand interaction detected (PLIP)

4 x 0GJ: L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide(Covalent)

0GJ.2: 15 residues within 4Å: Chain A: H.74, Q.117, D.218, S.219, C.220, Q.221, G.222, S.224, V.242, S.243, W.244, G.245, G.247, G.255 Ligands: CA.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.242 Hydrogen bonds: A:Q.117, A:S.219, A:G.222, A:D.223, A:S.224, A:S.243, A:G.245, A:G.245, A:G.247 Salt bridges: A:D.218 0GJ.4: 16 residues within 4Å: Chain B: H.74, Q.117, D.218, S.219, C.220, Q.221, G.222, D.223, S.224, V.242, S.243, W.244, G.245, G.247, G.255 Ligands: CA.3 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:V.242 Hydrogen bonds: B:Q.117, B:S.219, B:G.222, B:D.223, B:S.224, B:S.243, B:G.245, B:G.245, B:G.247 Salt bridges: B:D.218 0GJ.6: 15 residues within 4Å: Chain C: H.74, Q.117, D.218, S.219, C.220, Q.221, G.222, D.223, S.224, S.243, W.244, G.245, G.247, G.255 Ligands: CA.5 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:Q.117, C:S.219, C:S.219, C:G.222, C:D.223, C:S.224, C:S.243, C:G.245, C:G.247 Salt bridges: C:D.218 0GJ.7: 14 residues within 4Å: Chain D: H.74, Q.117, D.218, S.219, C.220, Q.221, G.222, S.224, V.242, S.243, W.244, G.245, G.247, G.255 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:V.242 Hydrogen bonds: D:Q.117, D:S.219, D:G.222, D:S.224, D:S.243, D:G.245, D:G.245 Salt bridges: D:D.218

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maun, H.R. et al., Bivalent antibody pliers inhibit beta-tryptase by an allosteric mechanism dependent on the IgG hinge. Nat Commun (2020)

Release Date

2020-12-30

Peptides

Tryptase alpha/beta-1: ABCD
Fab E104.v1 heavy chain: EGHJ
Fab E104.v1 light chain: FIKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
C

E
E

G
G

H
H

J
J

F
F

I
I

K
K

L
L

Tryptase alpha/beta-1

Fab E104.v1 heavy chain

Fab E104.v1 light chain