SMTL ID : 7zub.1

Cryo-EM structure of the indirubin-bound Hsp90-XAP2-AHR complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-1-mer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 25 residues within 4Å: Chain A: N.52, A.53, A.56, K.59, D.94, I.97, G.98, M.99, N.107, L.108, K.113, S.114, G.115, T.116, G.133, Q.134, F.135, G.136, V.137, G.138, F.139, T.185, V.187 Ligands: MG.2, MOO.3 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:N.52, A:K.59, A:D.94, A:N.107, A:S.114, A:G.115, A:T.116, A:T.116, A:T.116, A:G.133, A:F.135, A:G.136, A:V.137, A:G.138, A:F.139, A:T.185 ADP.4: 24 residues within 4Å: Chain B: N.52, A.53, A.56, K.59, D.94, I.97, G.98, M.99, N.107, L.108, K.113, S.114, G.115, T.116, G.133, Q.134, F.135, G.136, V.137, G.138, F.139, T.185 Ligands: MG.5, MOO.6 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:N.52, B:K.59, B:D.94, B:N.107, B:S.114, B:S.114, B:G.115, B:T.116, B:T.116, B:F.135, B:G.136, B:G.138, B:F.139, B:T.185

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: E.48, N.52, G.138 Ligands: ADP.1, MOO.3 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain B: N.52, G.138 Ligands: ADP.4, MOO.6 No protein-ligand interaction detected (PLIP)

2 x MOO: MOLYBDATE ION(Non-covalent)

MOO.3: 10 residues within 4Å: Chain A: E.48, G.133, Q.134, F.135, G.136, V.137, G.138, R.398 Ligands: ADP.1, MG.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.134, A:F.135, A:G.136, A:V.137, A:G.138, A:R.398 MOO.6: 11 residues within 4Å: Chain B: E.48, N.52, G.133, Q.134, F.135, G.136, V.137, G.138, R.398 Ligands: ADP.4, MG.5 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:E.48, B:Q.134, B:F.135, B:G.136, B:V.137, B:G.138, B:R.398, B:R.398

1 x JY6: (3~{Z})-3-(3-oxidanylidene-1~{H}-indol-2-ylidene)-1~{H}-indol-2-one(Non-covalent)

JY6.7: 20 residues within 4Å: Chain D: T.293, H.295, F.299, P.301, L.312, G.325, Y.326, F.328, I.329, C.337, A.338, S.340, H.341, S.350, I.353, F.355, L.357, S.369, V.385, Q.387 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:P.301, D:F.328, D:I.329, D:H.341, D:L.357 Hydrogen bonds: D:S.369, D:Q.387 pi-Stacking: D:H.295, D:H.295, D:F.299, D:F.299

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gruszczyk, J. et al., Cryo-EM structure of the agonist-bound Hsp90-XAP2-AHR cytosolic complex. Nat Commun (2022)

Release Date

2022-11-23

Peptides

Heat shock protein HSP 90-beta: AB
AH receptor-interacting protein: C
Aryl hydrocarbon receptor: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Heat shock protein HSP 90-beta

AH receptor-interacting protein

Aryl hydrocarbon receptor

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