SMTL ID : 7exp.1

Crystal structure of zebrafish TRAP1 with AMPPNP and MitoQ

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Covalent)(Non-covalent)

ANP.1: 22 residues within 4Å: Chain A: E.58, N.62, A.66, K.69, D.101, M.106, N.114, L.115, S.121, G.122, S.123, I.141, G.142, Q.143, F.144, G.145, V.146, G.147, F.148, T.194, R.345 Ligands: MG.2 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:E.58, A:N.62, A:K.69, A:D.101, A:S.121, A:S.121, A:S.121, A:G.122, A:S.123, A:Q.143, A:F.144, A:G.145, A:V.146, A:V.146, A:G.147, A:F.148 Water bridges: A:G.63, A:D.65, A:A.66, A:D.101, A:N.114, A:S.123, A:T.194, A:T.194, A:R.345, A:R.345 ANP.6: 23 residues within 4Å: Chain B: E.58, N.62, A.66, K.69, D.101, G.105, M.106, N.114, L.115, R.120, S.121, G.122, S.123, G.142, Q.143, F.144, G.145, V.146, G.147, F.148, T.194, R.345 Ligands: MG.7 24 PLIP interactions: 24 interactions with chain B Hydrogen bonds: B:N.62, B:D.65, B:K.69, B:D.101, B:S.121, B:G.122, B:S.123, B:Q.143, B:F.144, B:G.145, B:V.146, B:V.146, B:G.147, B:F.148, B:T.194, B:R.345, B:R.345 Water bridges: B:E.58, B:E.58, B:G.63, B:G.105, B:S.123, B:S.123, B:Y.149

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: N.62 Ligands: ANP.1 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain B: N.62 Ligands: ANP.6 No protein-ligand interaction detected (PLIP)

4 x CO: COBALT (II) ION(Non-covalent)

CO.3: 1 residues within 4Å: Chain A: L.130 No protein-ligand interaction detected (PLIP) CO.4: 2 residues within 4Å: Chain A: E.22, N.23 No protein-ligand interaction detected (PLIP) CO.8: 1 residues within 4Å: Chain B: M.433 No protein-ligand interaction detected (PLIP) CO.9: 2 residues within 4Å: Chain B: D.20, N.23 No protein-ligand interaction detected (PLIP)

1 x 05M: 2,3-dimethoxy-5-methyl-6-[10-(triphenyl-$l^{5}-phosphanyl)decyl]cyclohexa-2,5-diene-1,4-dione(Non-covalent)

05M.5: 10 residues within 4Å: Chain A: L.389, E.393, V.396, F.474, L.477 Chain B: F.296, R.328, L.389, E.393, F.474 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.389, B:F.296, B:F.474, B:F.474, B:F.474 pi-Stacking: A:F.474

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yoon, N.G. et al., Mitoquinone Inactivates Mitochondrial Chaperone TRAP1 by Blocking the Client Binding Site. J.Am.Chem.Soc. (2021)

Release Date

2022-01-05

Peptides

TNF receptor-associated protein 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

TNF receptor-associated protein 1

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