3INC | pdb_00003inc

Crystal structure of human insulin with Ni+2 complex

• PDB DOI: https://doi.org/10.2210/pdb3INC/pdb

• Classification: HORMONE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2009-08-12 Released: 2010-08-18 
• Deposition Author(s): Raghavendra, N., Pattabhi, V., Rajan, S.S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.257 (Depositor), 0.267 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Metal induced conformational changes in human insulin: Crystal structures of Sr+2, Ni+2 and Cu+2 complexes of human insulin

Raghavendra, N., Pattabhi, V., Rajan, S.S.

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 - A6B3C3 

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

Macromolecule Content 

• Total Structure Weight: 11.75 kDa 
• Atom Count: 861 
• 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	Homo sapiens	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	Homo sapiens	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	E [auth B], F [auth D]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.257 (Depositor), 0.267 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.654	α = 90
b = 81.654	β = 90
c = 33.767	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
AMoRE	phasing
REFMAC	refinement
AUTOMAR	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-08-18 
Deposition Author(s): Raghavendra, N., Pattabhi, V., Rajan, S.S.

Revision History  

• Version 1.0: 2010-08-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary