SMTL ID : 1tc0.2 (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-12-mer

Ligands

12 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) MG.19: 2 residues within 4Å: Chain E: N.43 Ligands: ATP.20 No protein-ligand interaction detected (PLIP) MG.24: 2 residues within 4Å: Chain F: N.43 Ligands: ATP.25 No protein-ligand interaction detected (PLIP) MG.28: 2 residues within 4Å: Chain G: N.43 Ligands: ATP.29 No protein-ligand interaction detected (PLIP) MG.33: 2 residues within 4Å: Chain H: N.43 Ligands: ATP.34 No protein-ligand interaction detected (PLIP) MG.37: 2 residues within 4Å: Chain I: N.43 Ligands: ATP.38 No protein-ligand interaction detected (PLIP) MG.42: 2 residues within 4Å: Chain J: N.43 Ligands: ATP.43 No protein-ligand interaction detected (PLIP) MG.46: 2 residues within 4Å: Chain K: N.43 Ligands: ATP.47 No protein-ligand interaction detected (PLIP) MG.51: 2 residues within 4Å: Chain L: N.43 Ligands: ATP.52 No protein-ligand interaction detected (PLIP)

12 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 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:N.43, C:D.85, C:N.98, C:F.135, C:T.181 Water bridges: C:A.47, C:K.50, C:D.85, C:D.85, C:Y.136 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 12 PLIP interactions: 10 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:N.43, D:D.85, D:F.135, D:T.181 Water bridges: D:E.39, D:E.39, D:E.39, D:N.43, D:A.47, D:G.134, C:K.31 Salt bridges: C:K.31 ATP.20: 11 residues within 4Å: Chain E: N.43, A.47, D.85, G.89, M.90, N.98, L.99, G.134, F.135, T.181 Ligands: MG.19 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:N.43, E:D.85, E:N.98, E:F.135, E:T.181 Water bridges: E:A.47, E:K.50, E:D.85, E:D.85, E:Y.136 ATP.25: 11 residues within 4Å: Chain E: K.31 Chain F: N.43, A.47, D.85, M.90, N.98, L.99, G.134, F.135, T.181 Ligands: MG.24 12 PLIP interactions: 10 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:N.43, F:D.85, F:F.135, F:T.181 Water bridges: F:E.39, F:E.39, F:E.39, F:N.43, F:A.47, F:G.134, E:K.31 Salt bridges: E:K.31 ATP.29: 11 residues within 4Å: Chain G: N.43, A.47, D.85, G.89, M.90, N.98, L.99, G.134, F.135, T.181 Ligands: MG.28 12 PLIP interactions: 12 interactions with chain G Hydrogen bonds: G:N.43, G:D.46, G:D.85, G:N.98, G:F.135 Water bridges: G:E.39, G:E.39, G:A.47, G:K.50, G:Y.136, G:T.181, G:T.181 ATP.34: 11 residues within 4Å: Chain G: K.31 Chain H: N.43, A.47, D.85, M.90, N.98, L.99, G.134, F.135, T.181 Ligands: MG.33 17 PLIP interactions: 15 interactions with chain H, 2 interactions with chain G Hydrogen bonds: H:N.43, H:D.85, H:N.98, H:F.135 Water bridges: H:E.39, H:E.39, H:N.43, H:D.46, H:A.47, H:D.85, H:D.85, H:G.134, H:G.134, H:T.181, H:T.181, G:K.31 Salt bridges: G:K.31 ATP.38: 11 residues within 4Å: Chain I: N.43, A.47, D.85, G.89, M.90, N.98, L.99, G.134, F.135, T.181 Ligands: MG.37 12 PLIP interactions: 12 interactions with chain I Hydrogen bonds: I:N.43, I:D.46, I:D.85, I:N.98, I:F.135 Water bridges: I:E.39, I:E.39, I:A.47, I:K.50, I:Y.136, I:T.181, I:T.181 ATP.43: 11 residues within 4Å: Chain I: K.31 Chain J: N.43, A.47, D.85, M.90, N.98, L.99, G.134, F.135, T.181 Ligands: MG.42 17 PLIP interactions: 15 interactions with chain J, 2 interactions with chain I Hydrogen bonds: J:N.43, J:D.85, J:N.98, J:F.135 Water bridges: J:E.39, J:E.39, J:N.43, J:D.46, J:A.47, J:D.85, J:D.85, J:G.134, J:G.134, J:T.181, J:T.181, I:K.31 Salt bridges: I:K.31 ATP.47: 11 residues within 4Å: Chain K: N.43, A.47, D.85, G.89, M.90, N.98, L.99, G.134, F.135, T.181 Ligands: MG.46 12 PLIP interactions: 12 interactions with chain K Hydrogen bonds: K:N.43, K:D.46, K:D.85, K:N.98, K:F.135 Water bridges: K:E.39, K:E.39, K:A.47, K:K.50, K:Y.136, K:T.181, K:T.181 ATP.52: 11 residues within 4Å: Chain K: K.31 Chain L: N.43, A.47, D.85, M.90, N.98, L.99, G.134, F.135, T.181 Ligands: MG.51 17 PLIP interactions: 15 interactions with chain L, 2 interactions with chain K Hydrogen bonds: L:N.43, L:D.85, L:N.98, L:F.135 Water bridges: L:E.39, L:E.39, L:N.43, L:D.46, L:A.47, L:D.85, L:D.85, L:G.134, L:G.134, L:T.181, L:T.181, K:K.31 Salt bridges: K:K.31

30 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 Ligand excluded by PLIP PG4.4: 2 residues within 4Å: Chain A: D.171, P.172 Ligand excluded by PLIP PG4.5: 4 residues within 4Å: Chain A: H.82, T.176, L.177 Ligands: PG4.3 Ligand excluded by PLIP PG4.8: 6 residues within 4Å: Chain B: T.148, R.173, L.177, T.182, T.184 Ligands: PG4.9 Ligand excluded by PLIP PG4.9: 3 residues within 4Å: Chain B: K.73, H.82 Ligands: PG4.8 Ligand excluded by PLIP PG4.12: 5 residues within 4Å: Chain C: I.146, T.148, R.173, T.184 Ligands: PG4.14 Ligand excluded by PLIP PG4.13: 2 residues within 4Å: Chain C: D.171, P.172 Ligand excluded by PLIP PG4.14: 4 residues within 4Å: Chain C: H.82, T.176, L.177 Ligands: PG4.12 Ligand excluded by PLIP PG4.17: 6 residues within 4Å: Chain D: T.148, R.173, L.177, T.182, T.184 Ligands: PG4.18 Ligand excluded by PLIP PG4.18: 3 residues within 4Å: Chain D: K.73, H.82 Ligands: PG4.17 Ligand excluded by PLIP PG4.21: 5 residues within 4Å: Chain E: I.146, T.148, R.173, T.184 Ligands: PG4.23 Ligand excluded by PLIP PG4.22: 2 residues within 4Å: Chain E: D.171, P.172 Ligand excluded by PLIP PG4.23: 4 residues within 4Å: Chain E: H.82, T.176, L.177 Ligands: PG4.21 Ligand excluded by PLIP PG4.26: 6 residues within 4Å: Chain F: T.148, R.173, L.177, T.182, T.184 Ligands: PG4.27 Ligand excluded by PLIP PG4.27: 3 residues within 4Å: Chain F: K.73, H.82 Ligands: PG4.26 Ligand excluded by PLIP PG4.30: 5 residues within 4Å: Chain G: I.146, T.148, R.173, T.184 Ligands: PG4.32 Ligand excluded by PLIP PG4.31: 2 residues within 4Å: Chain G: D.171, P.172 Ligand excluded by PLIP PG4.32: 4 residues within 4Å: Chain G: H.82, T.176, L.177 Ligands: PG4.30 Ligand excluded by PLIP PG4.35: 6 residues within 4Å: Chain H: T.148, R.173, L.177, T.182, T.184 Ligands: PG4.36 Ligand excluded by PLIP PG4.36: 3 residues within 4Å: Chain H: K.73, H.82 Ligands: PG4.35 Ligand excluded by PLIP PG4.39: 5 residues within 4Å: Chain I: I.146, T.148, R.173, T.184 Ligands: PG4.41 Ligand excluded by PLIP PG4.40: 2 residues within 4Å: Chain I: D.171, P.172 Ligand excluded by PLIP PG4.41: 4 residues within 4Å: Chain I: H.82, T.176, L.177 Ligands: PG4.39 Ligand excluded by PLIP PG4.44: 6 residues within 4Å: Chain J: T.148, R.173, L.177, T.182, T.184 Ligands: PG4.45 Ligand excluded by PLIP PG4.45: 3 residues within 4Å: Chain J: K.73, H.82 Ligands: PG4.44 Ligand excluded by PLIP PG4.48: 5 residues within 4Å: Chain K: I.146, T.148, R.173, T.184 Ligands: PG4.50 Ligand excluded by PLIP PG4.49: 2 residues within 4Å: Chain K: D.171, P.172 Ligand excluded by PLIP PG4.50: 4 residues within 4Å: Chain K: H.82, T.176, L.177 Ligands: PG4.48 Ligand excluded by PLIP PG4.53: 6 residues within 4Å: Chain L: T.148, R.173, L.177, T.182, T.184 Ligands: PG4.54 Ligand excluded by PLIP PG4.54: 3 residues within 4Å: Chain L: K.73, H.82 Ligands: PG4.53 Ligand excluded by PLIP

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: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

I
A

J
B

K
A

L
B

Endoplasmin

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