4L3T

Crystal Structure of Substrate-free Human Presequence Protease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.210
  • R-Value Work: 0.171

Literature

Macromolecules
Sequence Display for 4L3T

Classification: HYDROLASE

Total Structure Weight: 234463.89

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 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
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)
Modified Residues 3 Unique
ID Chains Type Formula 2D Diagram Parent
MLY
Query on MLY
A, B L-PEPTIDE LINKING C8 H18 N2 O2 LYS
CAS
Query on CAS
A, B L-PEPTIDE LINKING C5 H12 As N O2 S CYS
MLZ
Query on MLZ
A, B L-PEPTIDE LINKING C7 H16 N2 O2 LYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.210
  • R-Value Work: 0.171
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 245.78 α = 90.00
b = 85.09 β = 127.54
c = 158.46 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-06-06
  • Released Date: 2013-07-03
  • Deposition author(s): King, J.V., Liang, W.G., Tang, W.J.

Revision History

  • Version 1_0: 2013-07-03

    Type: Initial release

  • Version 1_1: 2014-05-14

    Type: Database references

  • Version 1_2: 2014-05-21

    Type: Database references

  • Version 1_3: 2014-07-09

    Type: Database references

  • Version 1_4: 2014-07-23

    Type: Database references