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

Transglutaminase 3 in complex with inhibitor Z-don and DH patient-derived Fab DH63-A02

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x P6S- ONL- VAL- PRO- MLL: P6S-ONL-VAL-PRO-MLL(Non-covalent)

P6S-ONL-VAL-PRO-MLL.1: 12 residues within 4Å: Chain B: I.174, W.237, R.248, Q.272, C.273, W.274, N.298, V.327, W.328, N.329, F.330, H.331 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:I.174, B:W.274, B:W.274, B:W.328, B:W.328, B:N.329, B:F.330 Hydrogen bonds: B:Q.272, B:C.273, B:V.327, B:N.329, B:N.329, B:N.329

1 x FLC: CITRATE ANION(Non-covalent)

FLC.2: 4 residues within 4Å: Chain B: S.413, V.414, N.415, H.417 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.413, B:V.414, B:V.414, B:N.415

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

EDO.3: 3 residues within 4Å: Chain B: N.169, R.170, I.171 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.171 EDO.8: 2 residues within 4Å: Chain C: S.7, G.8 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.8, C:T.112

3 x CA: CALCIUM ION(Non-covalent)

CA.4: 5 residues within 4Å: Chain B: A.222, N.225, S.226, N.227, D.229 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:A.222, B:N.225, B:N.227, B:D.229, H2O.1 CA.5: 5 residues within 4Å: Chain B: N.394, S.416, E.444, E.449, R.450 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.416, B:E.444, B:E.444, B:E.449, H2O.1 CA.6: 6 residues within 4Å: Chain B: D.302, D.304, N.306, S.308, D.310, D.325 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.302, B:D.304, B:S.308, B:D.310, B:D.325

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

PO4.7: 4 residues within 4Å: Chain B: H.21, W.138, H.149, R.152 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.152 Salt bridges: B:H.21, B:H.149

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

C
B

Antibody Fab fragment light chain IGKV4-1

Protein-glutamine gamma-glutamyltransferase E

Antibody Fab fragment heavy chain IGHV2-5

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