SMTL ID : 5hph.1

Structure of TRAP1 fragment

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.43 Å

Oligo State

homo-dimer

Ligands

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

ANP.1: 22 residues within 4Å: Chain A: E.61, N.65, A.69, K.72, D.104, M.109, N.117, L.118, R.123, S.124, G.125, S.126, G.145, Q.146, F.147, G.148, V.149, G.150, F.151, T.197, R.348 Ligands: MG.3 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:E.61, A:E.61, A:N.65, A:K.72, A:K.72, A:D.104, A:S.124, A:G.125, A:S.126, A:Q.146, A:F.147, A:G.148, A:V.149, A:G.150, A:F.151, A:T.197, A:R.348, A:R.348 Water bridges: A:N.65, A:N.65, A:D.68, A:D.68 ANP.6: 23 residues within 4Å: Chain B: E.61, N.65, A.69, K.72, D.104, G.108, M.109, N.117, L.118, R.123, S.124, G.125, S.126, G.145, Q.146, F.147, G.148, V.149, G.150, F.151, T.197, R.348 Ligands: MG.10 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:K.72, B:K.72, B:D.104, B:S.124, B:S.124, B:G.125, B:S.126, B:Q.146, B:F.147, B:G.148, B:V.149, B:G.150, B:F.151, B:R.348, B:R.348 Water bridges: B:N.65, B:N.117, B:N.117, B:T.197, B:T.197

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

PO4.2: 3 residues within 4Å: Chain A: Y.277, K.278, R.367 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.278 Salt bridges: A:R.367 PO4.7: 2 residues within 4Å: Chain B: Y.277, R.367 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.367, B:K.370 PO4.8: 7 residues within 4Å: Chain B: P.296, D.300, L.305, R.331, F.332, R.334, F.393 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.300 Salt bridges: B:R.334

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: E.61, N.65 Ligands: ANP.1 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain B: E.61, N.65 Ligands: ANP.6 No protein-ligand interaction detected (PLIP)

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: S.212, E.213, A.214 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.213, A:A.214 GOL.11: 6 residues within 4Å: Chain A: A.122, R.123, S.124, K.127 Chain B: E.39, K.42 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.123, A:S.124, B:E.39, B:K.42 GOL.12: 4 residues within 4Å: Chain B: S.211, S.212, E.213, A.214 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.213, B:A.214 GOL.13: 6 residues within 4Å: Chain A: E.39, K.42 Chain B: A.122, R.123, S.124, K.127 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.39, B:R.123, B:S.124

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

SO4.5: 3 residues within 4Å: Chain A: P.343, Q.352 Ligands: SO4.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.352 SO4.9: 8 residues within 4Å: Chain A: Q.352, E.353 Chain B: A.48, R.49, Y.52, K.55, M.156 Ligands: SO4.5 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.52, A:Q.352

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sung, N. et al., 2.4 angstrom resolution crystal structure of human TRAP1NM, the Hsp90 paralog in the mitochondrial matrix. Acta Crystallogr D Struct Biol (2016)

Release Date

2016-08-10

Peptides

Heat shock protein 75 kDa, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Heat shock protein 75 kDa, mitochondrial