SMTL ID : 8oxx.1

Transglutaminase 3 in complex with inhibitor Z-don and DH patient-derived Fab DH63-B02

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 6 residues within 4Å: Chain A: N.176, N.250, G.251, S.252, V.253, E.254 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.176, A:G.251, A:V.253, A:E.254 Water bridges: A:N.250, A:G.251

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

EDO.2: 4 residues within 4Å: Chain A: T.12, A.13, R.16, Q.27 No protein-ligand interaction detected (PLIP) EDO.3: 4 residues within 4Å: Chain A: K.23, S.25, F.180, E.181 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.25, A:S.25 Water bridges: A:F.180 EDO.12: 6 residues within 4Å: Chain B: S.129, V.130, F.131, P.132, K.218 Chain C: E.127 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.130, B:K.218 EDO.13: 6 residues within 4Å: Chain B: T.88, E.89, L.179, Q.180, S.181 Chain C: E.164 No protein-ligand interaction detected (PLIP) EDO.14: 10 residues within 4Å: Chain B: G.42, K.43, G.44 Chain C: H.8, D.88, Y.90, G.103, G.104, T.105, K.106 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:K.106, B:G.42 EDO.15: 5 residues within 4Å: Chain C: H.8, V.148, T.149, V.150, T.165 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:V.148, C:V.150, C:V.150 Water bridges: C:V.148

3 x CA: CALCIUM ION(Non-covalent)

CA.4: 7 residues within 4Å: Chain A: A.221, M.222, N.224, S.225, N.226, D.227, D.228 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:A.221, A:N.224, A:N.226, A:D.228, H2O.4 CA.5: 7 residues within 4Å: Chain A: N.393, S.415, H.416, K.440, E.443, E.448, R.449 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.415, A:E.443, A:E.448, H2O.2, H2O.3 CA.6: 8 residues within 4Å: Chain A: D.301, T.302, D.303, N.305, S.307, V.308, D.309, D.324 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.301, A:D.303, A:S.307, A:D.309, A:D.324

1 x P6S: benzyl hydrogen carbonate(Non-covalent)

P6S.7: 9 residues within 4Å: Chain A: V.164, I.173, R.247, Q.271, W.273, N.328, F.329 Ligands: ONL.8, DVA.9 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.273, A:F.329 Hydrogen bonds: A:N.328

1 x ONL: 5-OXO-L-NORLEUCINE(Covalent)

ONL.8: 13 residues within 4Å: Chain A: W.236, R.247, Q.271, C.272, W.273, W.327, N.328, F.329, H.330, V.331 Ligands: P6S.7, DVA.9, DPR.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.236, A:Q.271, A:C.272 Water bridges: A:Q.271

1 x DVA: D-VALINE(Non-covalent)

DVA.9: 8 residues within 4Å: Chain A: V.326, W.327, N.328, F.329 Ligands: P6S.7, ONL.8, DPR.10, MLL.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.328, A:N.328, A:N.328

1 x DPR: D-PROLINE(Non-covalent)

DPR.10: 6 residues within 4Å: Chain A: S.325, V.326, W.327 Ligands: ONL.8, DVA.9, MLL.11 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.327

1 x MLL: METHYL L-LEUCINATE(Non-covalent)

MLL.11: 6 residues within 4Å: Chain A: N.297, V.326, W.327, N.328 Ligands: DVA.9, DPR.10 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.326 Hydrogen bonds: A:V.326

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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