9MD8 | pdb_00009md8

Hip1 complex with inhibitor #2 (Hip1-2) via Ser228

• PDB DOI: https://doi.org/10.2210/pdb9MD8/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-12-05 Released: 2025-12-17 
• Deposition Author(s): Yim, M.K., Schumann, N.C., Goldfarb, N.E., Johnson, S.J.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.235 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Discovery of Highly Potent alpha-Keto Ester-Based Peptidomimetic Inhibitors of the Hip1 Protease for the Treatment of Mycobacterium tuberculosis

Schumann, N.C., Harris, H.T., Rouse Salcido, E.M., Brooks, C.L., Pena, K.J., Karakousis, P.C., Abell, A.D., Olsen, K.J., Yim, M.K., Johnson, S.J., Goldfarb, N.E.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 52.84 kDa 
• Atom Count: 3,837 
• Modeled Residue Count: 473 
• Deposited Residue Count: 486 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease	A	486	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: tap, ERS007688_01841 EC: 3.4 (PDB Primary Data), 3.4.14 (PDB Primary Data)
UniProt
Find proteins for A0A654TLU9 (Mycobacterium tuberculosis) Explore A0A654TLU9  Go to UniProtKB:  A0A654TLU9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1BK3	B [auth A]	N-carboxy-L-phenylalanyl-N-{(2S,3R)-3-hydroxy-4-methoxy-4-oxo-1-[(3R)-2-oxo-3,4-dihydro-2H-pyrrol-3-yl]butan-2-yl}-L-lysinamide C25 H35 N5 O8 WFSLHCGPTMFRHH-VYJAJWGXSA-N
GOL (Subject of Investigation/LOI)	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.235 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.725	α = 90
b = 103.725	β = 90
c = 127.189	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-17 
Deposition Author(s): Yim, M.K., Schumann, N.C., Goldfarb, N.E., Johnson, S.J.

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Funding Organization	Location	Grant Number
Other private	United States	--

Revision History  

• Version 1.0: 2025-12-17
  Type: Initial release