9IBB | pdb_00009ibb

Rhombohedral crystalline form of human insulin complexed with m-cresol

PDB DOI: https://doi.org/10.2210/pdb9IBB/pdb

Classification: HORMONE
Organism(s): Homo sapiens
Expression System: Saccharomyces cerevisiae
Mutation(s): No

Deposited: 2025-02-12 Released: 2025-10-29
Deposition Author(s): Papaefthymiou, C., Nanao, M.H., Margiolaki, I., Kontarinis, A., Kafetzi, S., Konstantopoulos, M., Koutoulas, D.
Funding Organization(s): Not funded

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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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

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.H., Margiolaki, I.

(2025) J Appl Crystallogr

DOI: https://doi.org/10.1107/S1600576725007484

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
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin A chain	A, C	21	Homo sapiens	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01308
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin B chain	B, D	30	Homo sapiens	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01308
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CRS (Subject of Investigation/LOI) Query on CRS Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth C] MOL2 format, chain E [auth A] MOL2 format, chain H [auth C] mmCIF format, chain E [auth A] mmCIF format, chain H [auth C]	E [auth A], H [auth C]	M-CRESOL C₇ H₈ O RLSSMJSEOOYNOY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth C] Interactions & Density Focus chain E [auth A] Focus chain H [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth C] MOL2 format, chain I [auth C] mmCIF format, chain I [auth C]	I [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth C] Interactions & Density Focus chain I [auth C]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain J [auth D] MOL2 format, chain G [auth B] MOL2 format, chain J [auth D] mmCIF format, chain G [auth B] mmCIF format, chain J [auth D]	G [auth B], J [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain J [auth D] Interactions & Density Focus chain G [auth B] Focus chain J [auth D]
SCN Query on SCN Download Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]