4AMT | pdb_00004amt

Crystal structure at 2.6A of human prorenin

• PDB DOI: https://doi.org/10.2210/pdb4AMT/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2012-03-13 Released: 2013-03-20 
• Deposition Author(s): Zhou, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.300 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.264 (Depositor), 0.280 (DCC) 
• R-Value Observed: 
  0.266 (Depositor) 

Starting Model: experimental

Literature

The Crystal Structure of Prorenin

Zhou, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 43.58 kDa 
• Atom Count: 2,799 
• Modeled Residue Count: 349 
• Deposited Residue Count: 383 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RENIN	A	383	Homo sapiens	Mutation(s): 0  EC: 3.4.23.15
UniProt & NIH Common Fund Data Resources
Find proteins for P00797 (Homo sapiens) Explore P00797  Go to UniProtKB:  P00797
PHAROS:  P00797 GTEx:  ENSG00000143839
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P00797-1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	B	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G32152BH GlyCosmos:  G32152BH GlyGen:  G32152BH

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.300 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.264 (Depositor), 0.280 (DCC) 
• R-Value Observed: 0.266 (Depositor) 

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.32	α = 90
b = 141.32	β = 90
c = 75.85	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-20 
Deposition Author(s): Zhou, A.

Revision History  

• Version 1.0: 2013-03-20
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
• Version 2.1: 2023-12-20
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-10-23
  Changes: Structure summary