3JSD | pdb_00003jsd

Insulin's biosynthesis and activity have opposing structural requirements: a new factor in neonatal diabetes mellitus

• PDB DOI: https://doi.org/10.2210/pdb3JSD/pdb

• Classification: HORMONE
• Organism(s): Homo sapiens
• Mutation(s): Yes 


• Deposited: 2009-09-10 Released: 2010-09-15 
• Deposition Author(s): Weiss, M.A., Wan, Z.L., Dodson, E.J., Liu, M., Xu, B., Hua, Q.X., Turkenburg, M., Whittingham, J., Nakagawa, S.H., Huang, K., Hu, S.Q., Jia, W.H., Wang, S.H., Brange, J., Whittaker, J., Arvan, P., Katsoyannis, P.G., Dodson, G.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.274 (Depositor) 
• R-Value Work: 
  0.206 (Depositor) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Insulin's biosynthesis and activity have opposing structural requirements: a new factor in neonatal diabetes mellitus

Weiss, M.A., Wan, Z.L., Dodson, E.J., Liu, M., Xu, B., Hua, Q.X., Turkenburg, M., Whittingham, J., Nakagawa, S.H., Huang, K., Hu, S.Q., Jia, W.H., Wang, S.H., Brange, J., Whittaker, J., Arvan, P., Katsoyannis, P.G., Dodson, G.G.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A6B6 Pseudo Symmetry: Cyclic - C3  (Explore in 3D)
Pseudo Stoichiometry: Hetero 12-mer - A3B3C3D3 

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

Macromolecule Content 

• Total Structure Weight: 11.96 kDa 
• Atom Count: 841 
• Modeled Residue Count: 102 
• Deposited Residue Count: 102 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin A chain	A, C	21	N/A	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01308 (Homo sapiens) Explore P01308  Go to UniProtKB:  P01308
PHAROS:  P01308 GTEx:  ENSG00000254647

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin B chain	B, D	30	N/A	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for P01308 (Homo sapiens) Explore P01308  Go to UniProtKB:  P01308
PHAROS:  P01308 GTEx:  ENSG00000254647

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IPH	G [auth C]	PHENOL C6 H6 O ISWSIDIOOBJBQZ-UHFFFAOYSA-N
ZN	E [auth B], H [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	F [auth B], I [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.274 (Depositor) 
• R-Value Work:  0.206 (Depositor) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.843	α = 90
b = 80.843	β = 90
c = 38.842	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
CNS	refinement
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-15 
Deposition Author(s): Weiss, M.A., Wan, Z.L., Dodson, E.J., Liu, M., Xu, B., Hua, Q.X., Turkenburg, M., Whittingham, J., Nakagawa, S.H., Huang, K., Hu, S.Q., Jia, W.H., Wang, S.H., Brange, J., Whittaker, J., Arvan, P., Katsoyannis, P.G., Dodson, G.G.

Revision History  

• Version 1.0: 2010-09-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2021-10-13
  Changes: Database references, Derived calculations
• Version 1.4: 2023-09-06
  Changes: Data collection, Refinement description
• Version 1.5: 2024-10-30
  Changes: Structure summary