4RPU

Crystal Structure of Human Presequence Protease in Complex with Inhibitor MitoBloCK-60

• PDB DOI: https://doi.org/10.2210/pdb4RPU/pdb

• Classification: hydrolase/hydrolase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-10-31 Released: 2015-12-09 
• Deposition Author(s): Mo, S.M., Liang, W.G., King, J.V., Wijaya, J., Koehler, C.M., Tang, W.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 0.208 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 

Literature

Crystal Structure of Human Presequence Protease in Complex with Inhibitor MitoBloCK-60

Mo, S.M., Liang, W.G., King, J.V., Wijaya, J., Koehler, C.M., Tang, W.J.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 235.62 kDa 
• Atom Count: 16,942 
• Modelled Residue Count: 1,967 
• Deposited Residue Count: 2,028 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Presequence protease, mitochondrial	A	1,014	Homo sapiens	Mutation(s): 1  Gene Names: PITRM1, KIAA1104, MP1 EC: 3.4.24
UniProt & NIH Common Fund Data Resources
Find proteins for Q5JRX3 (Homo sapiens) Explore Q5JRX3  Go to UniProtKB:  Q5JRX3
PHAROS:  Q5JRX3 GTEx:  ENSG00000107959

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Presequence protease, mitochondrial	B	1,014	Homo sapiens	Mutation(s): 1  Gene Names: PITRM1, KIAA1104, MP1 EC: 3.4.24
UniProt & NIH Common Fund Data Resources
Find proteins for Q5JRX3 (Homo sapiens) Explore Q5JRX3  Go to UniProtKB:  Q5JRX3
PHAROS:  Q5JRX3 GTEx:  ENSG00000107959

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3UE	D [auth A], E [auth A], U [auth B], V [auth B]	[4-(diphenylmethyl)piperazin-1-yl](3-methyl-4-nitrophenyl)methanone C25 H25 N3 O3 FJZPDGSOVGNVJO-UHFFFAOYSA-N
GOL	AA [auth B], BA [auth B], CA [auth B], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], W [auth B], X [auth B], Y [auth B], Z [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	C [auth A], T [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	DA [auth B], EA [auth B], FA [auth B], GA [auth B], HA [auth B], Q [auth A], R [auth A], S [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	IA [auth B], JA [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CAS	A	L-PEPTIDE LINKING	C5 H12 As N O2 S		CYS
MLY	A	L-PEPTIDE LINKING	C8 H18 N2 O2		LYS
MLZ	A	L-PEPTIDE LINKING	C7 H16 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 0.208 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 245.624	α = 90
b = 85.49	β = 127.53
c = 158.214	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
PHASER	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-12-09 
Deposition Author(s): Mo, S.M., Liang, W.G., King, J.V., Wijaya, J., Koehler, C.M., Tang, W.J.

Revision History  

• Version 1.0: 2015-12-09
  Type: Initial release