SMTL ID : 1tc0.3 (2 other biounits)

Ligand Induced Conformational Shifts in the N-terminal Domain of GRP94, Open Conformation Complexed with the physiological partner ATP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: N.43 Ligands: ATP.2 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain B: N.43 Ligands: ATP.7 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain C: N.43 Ligands: ATP.11 No protein-ligand interaction detected (PLIP) MG.15: 2 residues within 4Å: Chain D: N.43 Ligands: ATP.16 No protein-ligand interaction detected (PLIP)

4 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 11 residues within 4Å: Chain A: N.43, A.47, D.85, G.89, M.90, N.98, L.99, G.134, F.135, T.181 Ligands: MG.1 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.43, A:D.85, A:N.98, A:F.135, A:T.181 Water bridges: A:A.47, A:K.50, A:D.85, A:D.85, A:Y.136 ATP.7: 11 residues within 4Å: Chain A: K.31 Chain B: N.43, A.47, D.85, M.90, N.98, L.99, G.134, F.135, T.181 Ligands: MG.6 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.43, B:D.85, B:F.135, B:T.181 Water bridges: B:E.39, B:E.39, B:E.39, B:N.43, B:A.47, B:G.134, A:K.31 Salt bridges: A:K.31 ATP.11: 11 residues within 4Å: Chain C: N.43, A.47, D.85, G.89, M.90, N.98, L.99, G.134, F.135, T.181 Ligands: MG.10 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:N.43, C:D.46, C:D.85, C:N.98, C:F.135 Water bridges: C:E.39, C:E.39, C:A.47, C:K.50, C:Y.136, C:T.181, C:T.181 ATP.16: 11 residues within 4Å: Chain C: K.31 Chain D: N.43, A.47, D.85, M.90, N.98, L.99, G.134, F.135, T.181 Ligands: MG.15 17 PLIP interactions: 15 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:N.43, D:D.85, D:N.98, D:F.135 Water bridges: D:E.39, D:E.39, D:N.43, D:D.46, D:A.47, D:D.85, D:D.85, D:G.134, D:G.134, D:T.181, D:T.181, C:K.31 Salt bridges: C:K.31

10 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.3: 5 residues within 4Å: Chain A: I.146, T.148, R.173, T.184 Ligands: PG4.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.173, A:R.173 Water bridges: A:T.184 PG4.4: 2 residues within 4Å: Chain A: D.171, P.172 No protein-ligand interaction detected (PLIP) PG4.5: 4 residues within 4Å: Chain A: H.82, T.176, L.177 Ligands: PG4.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.177 Hydrogen bonds: A:H.82 Water bridges: A:T.84 PG4.8: 6 residues within 4Å: Chain B: T.148, R.173, L.177, T.182, T.184 Ligands: PG4.9 2 PLIP interactions: 2 interactions with chain B Water bridges: B:T.148, B:T.184 PG4.9: 3 residues within 4Å: Chain B: K.73, H.82 Ligands: PG4.8 2 PLIP interactions: 2 interactions with chain B Water bridges: B:K.73, B:T.84 PG4.12: 5 residues within 4Å: Chain C: I.146, T.148, R.173, T.184 Ligands: PG4.14 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.148, C:R.173, C:R.173, C:T.184 PG4.13: 2 residues within 4Å: Chain C: D.171, P.172 No protein-ligand interaction detected (PLIP) PG4.14: 4 residues within 4Å: Chain C: H.82, T.176, L.177 Ligands: PG4.12 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.177 PG4.17: 6 residues within 4Å: Chain D: T.148, R.173, L.177, T.182, T.184 Ligands: PG4.18 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.148 Water bridges: D:T.148 PG4.18: 3 residues within 4Å: Chain D: K.73, H.82 Ligands: PG4.17 1 PLIP interactions: 1 interactions with chain D Water bridges: D:K.73

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Immormino, R.M. et al., Ligand-induced Conformational Shift in the N-terminal Domain of GRP94, an Hsp90 Chaperone. J.Biol.Chem. (2004)

Release Date

2004-08-24

Peptides

Endoplasmin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Endoplasmin

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