9IBB | pdb_00009ibb

Rhombohedral crystalline form of human insulin complexed with m-cresol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 
    0.224 (Depositor), 0.224 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.178 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Exploring humidity effects on polycrystalline human insulin-ligand complexes: preliminary crystallographic insights.

Kontarinis, A.Papaefthymiou, C.Kafetzi, S.Konstantopoulos, M.Koutoulas, D.Nanao, M.Schluckebier, G.Norrman, M.Dadivanyan, N.Beckers, D.Degen, T.Rosmaraki, E.Fitch, A.Margiolaki, I.

(2025) J Appl Crystallogr 58: 1920-1935

  • DOI: https://doi.org/10.1107/S1600576725007484
  • Primary Citation Related Structures: 
    9IBB, 9QLD

  • PubMed Abstract: 

    This study investigates the effect of relative humidity (RH) on the crystal structures of human insulin (HI) complexes with organic ligands, m -cresol and m -nitro-phenol, using in situ X-ray powder diffraction (XRPD) with a controlled-humidity chamber. Co-crystallization at pH 7.5 produced hexagonal microcrystals (space group R 3) for both protein-ligand complexes. The corresponding single-crystal X-ray diffraction structures were solved: HI- m -cresol (PDB entry 9ibb, 1.84 Å) and HI- m -nitro-phenol (PDB entry 9qld, 2.55 Å). Pawley analysis of the in situ XRPD data revealed structural stability up to 70% RH, with no phase transitions observed. At lower humidity levels, reduced diffraction intensities indicated loss of crystallinity, which was fully restored upon rehydration to 95% RH. Notably, each complex exhibited distinct changes in unit-cell parameters during dehydration-rehydration cycles. These results highlight the critical role of controlling environmental factors in structure-based drug design and pharmaceutical manufacturing, and demonstrate how organic ligands can enhance the stability of protein crystals, offering valuable insights for pharmaceutical development.


  • Organizational Affiliation
    • Department of Biology, Section of Genetics, Cell Biology and Development University of Patras Patras GR-26500 Greece.

Macromolecule Content 

  • Total Structure Weight: 12.13 kDa 
  • Atom Count: 806 
  • Modeled Residue Count: 97 
  • Deposited Residue Count: 102 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Insulin A chain
A, C
21Homo sapiensMutation(s): 0 
Gene Names: INS
UniProt & NIH Common Fund Data Resources
Find proteins for P01308 (Homo sapiens)
Explore P01308 
Go to UniProtKB:  P01308
PHAROS:  P01308
GTEx:  ENSG00000254647 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01308
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Insulin B chain
B, D
30Homo sapiensMutation(s): 0 
Gene Names: INS
UniProt & NIH Common Fund Data Resources
Find proteins for P01308 (Homo sapiens)
Explore P01308 
Go to UniProtKB:  P01308
PHAROS:  P01308
GTEx:  ENSG00000254647 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01308
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CRS
(Subject of Investigation/LOI)

Query on CRS



Download:Ideal Coordinates CCD File
E [auth A],
H [auth C]
M-CRESOL
C7 H8 O
RLSSMJSEOOYNOY-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
I [auth C]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
G [auth B],
J [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
SCN

Query on SCN



Download:Ideal Coordinates CCD File
F [auth B]THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free:  0.224 (Depositor), 0.224 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.178 (DCC) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.684α = 90
b = 78.684β = 90
c = 39.883γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-29
    Type: Initial release
  • Version 1.1: 2026-01-28
    Changes: Database references