SMTL ID : 8oxy.1

Transglutaminase 3 without calcium in complex with DH patient-derived Fab DH63-B02

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

EDO.1: 12 residues within 4Å: Chain A: R.245, S.249, W.250, N.251, E.255, M.631, V.632, E.633, N.641, K.643, L.672, D.674 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.245, A:R.245, A:N.251, A:E.255, A:E.633, A:K.643 Water bridges: A:N.251 EDO.2: 10 residues within 4Å: Chain A: A.222, M.223, N.225, S.226, N.227, D.228, N.230, G.231, F.365 Ligands: EDO.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.226, A:S.226, A:N.227, A:N.227, A:D.228, A:D.228, A:G.231 EDO.3: 8 residues within 4Å: Chain A: S.196, L.197, N.198, R.201, V.219, A.222, M.223 Ligands: EDO.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.196, A:L.197, A:N.198, A:N.198 Water bridges: A:R.201 EDO.4: 11 residues within 4Å: Chain A: P.481, S.482, I.483, V.515, C.576, K.577, V.578, E.581, S.582, E.583, V.584 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.482, A:I.483, A:I.483, A:V.578, A:S.582 EDO.5: 6 residues within 4Å: Chain A: R.34, A.104, S.105, V.141, D.142, S.143 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.34, A:S.143, A:S.143 Water bridges: A:R.34, A:R.34, A:N.211 EDO.6: 10 residues within 4Å: Chain A: S.299, A.300, H.301, W.328, H.331, W.333, T.356, P.357, F.388, E.392 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.301, A:E.392, A:E.392 EDO.8: 9 residues within 4Å: Chain C: H.8, S.9, A.147, V.148, T.149, T.200, H.201, E.202, G.203 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:H.8, C:G.203 Water bridges: C:H.8, C:S.9, C:S.9, C:E.202 EDO.9: 7 residues within 4Å: Chain A: G.264 Chain C: R.24, S.31, N.32, Y.94, D.95, P.96 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.24, C:R.24, C:N.32, C:N.32 EDO.10: 5 residues within 4Å: Chain C: S.13, L.110, G.111, Q.112, P.113 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.112 EDO.11: 11 residues within 4Å: Chain B: F.131, P.132, L.133, L.150 Chain C: F.122, P.123, P.124, S.125, E.128, T.135, V.137 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:P.123, C:S.125, C:S.125 EDO.12: 9 residues within 4Å: Chain B: A.146, V.190, T.192 Chain C: S.118, V.119, T.120, L.139, I.140, S.141 No protein-ligand interaction detected (PLIP)

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

PO4.7: 7 residues within 4Å: Chain A: Y.241, T.242, G.244, R.245, D.246 Chain B: D.31, L.102 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.241 Water bridges: A:Y.241, A:Y.241, A:D.246

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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