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

Transglutaminase 3 in complex with DH patient-derived Fab DH63-A02

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-1-1-1-mer

Ligands

5 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 2 residues within 4Å: Chain B: D.1, Q.27 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.27 PO4.5: 4 residues within 4Å: Chain C: N.415, H.417, T.418, R.421 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.415, C:T.418, C:R.421 Salt bridges: C:H.417 PO4.6: 5 residues within 4Å: Chain C: H.21, K.24, E.153, Q.157 Ligands: PO4.7 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.153, C:Q.157 PO4.7: 6 residues within 4Å: Chain C: H.21, W.138, H.149, R.152, E.153 Ligands: PO4.6 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.153 Salt bridges: C:H.21, C:H.149, C:R.152 PO4.8: 2 residues within 4Å: Chain C: N.227, D.228 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.228, C:D.228

3 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain C: A.222, N.225, N.227, D.229 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:A.222, C:N.225, C:N.227, C:D.229, C:D.229 CA.3: 5 residues within 4Å: Chain C: N.394, S.416, E.444, E.449, R.450 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:S.416, C:E.444, C:E.444, C:E.449, H2O.2 CA.4: 6 residues within 4Å: Chain C: D.302, D.304, N.306, S.308, D.310, D.325 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.302, C:D.304, C:S.308, C:D.310, C:D.325

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Iversen, R. et al., Enzyme-activating B-cell receptors boost antigen presentation to pathogenic T cells in gluten-sensitive autoimmunity. Nat Commun (2025)

Release Date

2025-03-12

Peptides

Antibody Fab fragment heavy chain IGHV2-5: A
Antibody Fab fragment light chain IGKV4-1: B
Protein-glutamine gamma-glutamyltransferase E: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
D

Antibody Fab fragment heavy chain IGHV2-5

Antibody Fab fragment light chain IGKV4-1

Protein-glutamine gamma-glutamyltransferase E

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