9D9I: Human Hsp90b nucleotide binding domain

Human Hsp90b nucleotide binding domain in complex with BRI2312. Determined by X-ray diffraction at 1.5 Å resolution. Released 10 Sept 2025.

Method: X-ray diffraction
Resolution: 1.5 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,262
Mol. weight: 25.92 kDa
Ligands: A1A24
Released: 10 Sept 2025

Explore 9D9I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9D9I contains 11 α-helices and 8 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 11 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	13-16	4	1
α-helix	17-18	2
α-helix	19-30	12
α-helix	38-58	21
α-helix	62-65	4
β-strand	73-78	6	1
β-strand	83-88	6	1
α-helix	95-96	2
α-helix	97-101	5
α-helix	102-118	17
α-helix	123-129	7
α-helix	132-138	7
β-strand	140-148	9	1
β-strand	155-159	5	1
β-strand	164-169	6	1
β-strand	178-185	8	1
α-helix	187-193	7
α-helix	195-205	11
β-strand	213-215	3	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Heat shock protein HSP 90-beta	A	protein	224	Homo sapiens	P08238 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9D9I_1 Heat shock protein HSP 90-beta (chains A)
GMPEEVHHGEEEVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNASDALDKIRYESL
TDPSKLDSGKELKIDIIPNPQERTLTLVDTGIGMTKADLINNLGTIAKSGTKAFMEALQA
GADISMIGQFGVGFYSAYLVAEKVVVITKHNDDEQYAWESSAGGSFTVRADHGEPIGRGT
KVILHLKEDQTEYLEERRVKEVVKKHSQFIGYPITLYLEKEREK

Ligands and cofactors

ID	Name	Formula	Copies
A1A24	(1P)-3-amino-6-[({1-[(2R)-2-(2,4-difluorophenyl)-2-hydroxy-3-(1H-1,2,4-triazol-…	C37 H37 F2 N9 O3 S	1

Water and common crystallization additives (CL) are not listed.

Primary citation

Human Hsp90b nucleotide binding domain in complex with BRI2312. Kuntz, D.A., Prive, G.G. To be published.

Other PDB entries of the same protein (UniProt P08238 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6N8Y 1.55 Å, Hsp90-beta bound to PU-11-trans
5UCJ 1.69 Å, Hsp90b N-terminal domain with inhibitors
7ULJ 1.82 Å, Hsp90b N-terminal domain in complex with 42C
9D9H 1.96 Å, Human Hsp90b nucleotide binding domain in complex with BRI2311
5UC4 2.05 Å, Hsp90b N-terminal domain with inhibitors
3FWV 2.2 Å, Crystal Structure of a Redesigned TPR Protein, T-MOD(VMY), in Complex with MEEVF Peptide
3NMQ 2.2 Å, Hsp90b N-terminal domain in complex with EC44, a pyrrolo-pyrimidine methoxypyridine…
3PRY 2.28 Å, Crystal structure of the middle domain of human HSP90-beta refined at 2.3 A resolution
1UYM 2.45 Å, Human Hsp90-beta with PU3 (9-Butyl-8(3,4,5-trimethoxy-benzyl)-9H-purin-6-ylamine)
3UQ3 2.6 Å, TPR2AB-domain:pHSP90-complex of yeast Sti1
9W5I 2.63 Å, AGO maturation complex (AMC): AGO2-miRNA duplex in complex with Hsp90 beta and…
5UCH 2.65 Å, Hsp90b N-terminal domain with inhibitors

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