SMTL ID : 8oxv.1

Transglutaminase 3 zymogen in complex with DH patient-derived Fab DH63-B02

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-1-mer

Ligands

3 x CA: CALCIUM ION(Non-covalent)

CA.1: 7 residues within 4Å: Chain A: A.222, M.223, N.225, S.226, N.227, D.228, D.229 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:A.222, A:N.225, A:N.227, A:D.229, A:D.229 CA.2: 7 residues within 4Å: Chain A: N.394, S.416, H.417, K.441, E.444, E.449, R.450 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.416, A:E.444, A:E.449, H2O.9, H2O.14 CA.3: 7 residues within 4Å: Chain A: D.302, T.303, D.304, N.306, S.308, V.309, D.325 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.302, A:D.304, A:S.308, A:D.325, H2O.9

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 6 residues within 4Å: Chain A: N.169, R.170, L.493, R.588, I.590, I.591 Ligand excluded by PLIP

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 6 residues within 4Å: Chain B: P.156, E.157, P.158, K.210, P.211 Ligands: EDO.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.157 EDO.6: 3 residues within 4Å: Chain B: K.210, P.211 Ligands: EDO.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.210 Water bridges: B:P.211 EDO.7: 7 residues within 4Å: Chain C: Q.38, R.40, T.46, V.48, V.59, P.60, F.63 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.38, C:R.40, C:R.40 Water bridges: C:T.46, C:G.58

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Heggelund, J.E. et al., Autoantibody binding and unique enzyme-substrate intermediate conformation of human transglutaminase 3. Nat Commun (2023)

Release Date

2023-10-18

Peptides

Protein-glutamine gamma-glutamyltransferase E 27 kDa non-catalytic chain: A
Antibody Fab fragment Heavy chain: B
Antibody Fab fragment light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Protein-glutamine gamma-glutamyltransferase E 27 kDa non-catalytic chain

Antibody Fab fragment Heavy chain

Antibody Fab fragment light chain

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