SMTL ID : 8oxw.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: W.11, L.30, G.129, T.130 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.130, A:T.130 Water bridges: A:W.11, A:L.30 EDO.2: 9 residues within 4Å: Chain A: R.245, S.249, W.250, N.251, E.255, M.631, E.633, N.641, D.674 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.249, A:N.251, A:E.633 Water bridges: A:R.245, A:N.251, A:N.641 EDO.3: 6 residues within 4Å: Chain A: D.212, K.214, Y.215, R.218, P.369, F.384 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.218 EDO.4: 6 residues within 4Å: Chain A: R.34, A.104, S.105, V.141, D.142, S.143 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.141, A:S.143 Water bridges: A:R.34, A:V.141 EDO.5: 5 residues within 4Å: Chain A: S.346, Y.347, I.373, E.377, D.379 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.346, A:S.346 Water bridges: A:S.346, A:Y.347 EDO.6: 4 residues within 4Å: Chain A: I.57, S.59, P.64, K.71 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.71 EDO.7: 6 residues within 4Å: Chain A: H.21, W.138, F.145, R.152 Ligands: EDO.8, EDO.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.152 Water bridges: A:H.21 EDO.8: 6 residues within 4Å: Chain A: H.21, Q.36, N.136, W.138, L.139 Ligands: EDO.7 No protein-ligand interaction detected (PLIP) EDO.9: 5 residues within 4Å: Chain A: G.147, N.148, H.149, R.152 Ligands: EDO.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.147, A:H.149, A:R.152 EDO.10: 7 residues within 4Å: Chain A: W.337, P.345, S.346, Y.347, G.348, G.349, I.373 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.348 Water bridges: A:P.345 EDO.15: 10 residues within 4Å: Chain B: A.146, F.175, V.190, T.192 Chain C: S.118, V.119, T.120, L.139, I.140, S.141 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:T.192, C:S.118 Water bridges: C:S.118

3 x CA: CALCIUM ION(Non-covalent)

CA.11: 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.12: 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.10, H2O.12 CA.13: 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.7

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

CL.14: 6 residues within 4Å: Chain A: N.169, R.170, L.493, R.588, I.590, I.591 Ligand excluded by PLIP

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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