4RPU | pdb_00004rpu

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free:
0.208 (Depositor), 0.211 (DCC)
R-Value Work:
0.175 (Depositor), 0.181 (DCC)
R-Value Observed:
0.176 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5JRX3
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5JRX3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3UE Query on 3UE Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain U [auth B] SDF format, chain V [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B]	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		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain U [auth B] Focus chain V [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	AA [auth B] BA [auth B] CA [auth B] F [auth A] G [auth A] 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		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain T [auth B] MOL2 format, chain C [auth A] MOL2 format, chain T [auth B] mmCIF format, chain C [auth A] mmCIF format, chain T [auth B]	C [auth A], T [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain T [auth B] Interactions & Density Focus chain C [auth A] Focus chain T [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A]	DA [auth B] EA [auth B] FA [auth B] GA [auth B] HA [auth B] 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		Interactions Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Interactions & Density Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain IA [auth B] SDF format, chain JA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain JA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain JA [auth B]	IA [auth B], JA [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain IA [auth B] Focus chain JA [auth B] Interactions & Density Focus chain IA [auth B] Focus chain JA [auth B]

Modified Residues 3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CAS Query on CAS	A	L-PEPTIDE LINKING	C₅ H₁₂ As N O₂ S		CYS
MLY Query on MLY	A	L-PEPTIDE LINKING	C₈ H₁₈ N₂ O₂		LYS
MLZ Query on 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 (Depositor), 0.211 (DCC)
R-Value Work: 0.175 (Depositor), 0.181 (DCC)
R-Value Observed: 0.176 (Depositor)

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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-12-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-12-09
Type: Initial release
Version 1.1: 2025-03-26
Changes: Data collection, Database references, Derived calculations, Structure summary