4RPU

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


Experimental Data Snapshot

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

Literature

Macromolecules
Sequence Display for 4RPU

Classification: hydrolase / hydrolase inhibitor

Total Structure Weight: 235620.44

Macromolecule Entities
Molecule Chains Length Organism Details
Presequence protease, mitochondrial A 1014 Homo sapiens EC#: 3.4.24 IUBMB
Fragment: UNP residues 33-1037
Mutation: E107Q, I328V, A397V, Q1037R
Gene Name(s): PITRM1 Gene View KIAA1104 MP1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Presequence protease, mitochondrial B 1014 Homo sapiens EC#: 3.4.24 IUBMB
Fragment: UNP residues 33-1037
Mutation: E107Q, I328V, A397V, Q1037R
Gene Name(s): PITRM1 Gene View KIAA1104 MP1

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
3UE
Query on 3UE

A, B [4-(diphenylmethyl)piperazin-1-yl](3-methyl- 4-nitrophenyl)methanone
C25 H25 N3 O3
FJZPDGSOVGNVJO-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

A, B ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

B CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 3 Unique
ID Chains Type Formula 2D Diagram Parent
MLZ
Query on MLZ
A, B L-PEPTIDE LINKING C7 H16 N2 O2 LYS
CAS
Query on CAS
A, B L-PEPTIDE LINKING C5 H12 As N O2 S CYS
MLY
Query on MLY
A, B L-PEPTIDE LINKING C8 H18 N2 O2 LYS

Experimental Data & Validation

Experimental Data

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

Unit Cell:

Length (Å) Angle (°)
a = 245.62 α = 90.00
b = 85.49 β = 127.53
c = 158.21 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2014-10-31
  • 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