4RPU

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.265 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.0 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.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Presequence protease, mitochondrial
A
1014Homo sapiensGene Names: PITRM1 (KIAA1104, MP1)
EC: 3.4.24.-
Find proteins for Q5JRX3 (Homo sapiens)
Go to Gene View: PITRM1
Go to UniProtKB:  Q5JRX3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Presequence protease, mitochondrial
B
1014Homo sapiensGene Names: PITRM1 (KIAA1104, MP1)
EC: 3.4.24.-
Find proteins for Q5JRX3 (Homo sapiens)
Go to Gene View: PITRM1
Go to UniProtKB:  Q5JRX3
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
3UE
Query on 3UE

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A, B
[4-(diphenylmethyl)piperazin-1-yl](3-methyl-4-nitrophenyl)methanone
C25 H25 N3 O3
FJZPDGSOVGNVJO-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
MLZ
Query on MLZ
A, B
L-PEPTIDE LINKINGC7 H16 N2 O2LYS
CAS
Query on CAS
A, B
L-PEPTIDE LINKINGC5 H12 As N O2 SCYS
MLY
Query on MLY
A, B
L-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.265 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.175 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 245.624α = 90.00
b = 85.490β = 127.53
c = 158.214γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data collection
HKL-3000data scaling
PHASERphasing
PHENIXrefinement
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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