6GNQ | pdb_00006gnq

Monoclinic crystalline form of human insulin, complexed with meta-cresol

PDB DOI: https://doi.org/10.2210/pdb6GNQ/pdb

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

Deposited: 2018-05-31 Released: 2019-06-12
Deposition Author(s): Margiolaki, I., Karavassili, F., Valmas, A., Dimarogona, M., Giannopoulou, A.E., Fili, S., Schluckebier, G., Norrman, M., Beckers, D., Fitch, A.N.
Funding Organization(s): European Union, "General Secretariat for Research and Technology (GSRT) - Hellenic Foundation for Research and Innovation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.279 (Depositor), 0.276 (DCC)
R-Value Work:
0.223 (Depositor), 0.226 (DCC)
R-Value Observed:
0.226 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Monoclinic crystalline form of human insulin, complexed with meta-cresol

Margiolaki, I., Karavassili, F., Valmas, A., Dimarogona, M., Giannopoulou, A.E., Fili, S., Schluckebier, G., Norrman, M., Beckers, D., Fitch, A.N.

To be published.

Macromolecule Content

Total Structure Weight: 72.23 kDa
Atom Count: 4,901
Modeled Residue Count: 588
Deposited Residue Count: 612
Unique protein chains: 2

Macromolecules

Find similar proteins by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin	A, C, E, G, I A, C, E, G, I, K, M, O, Q, S, U, W	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01308
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin	B, D, F, H, J B, D, F, H, J, L, N, P, R, T, V, X	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 AB [auth U] SDF format, chain BB [auth W] SDF format, chain CA [auth C] SDF format, chain GA [auth E] SDF format, chain JA [auth G] SDF format, chain NA [auth K] SDF format, chain OA [auth M] SDF format, chain RA [auth O] SDF format, chain VA [auth Q] SDF format, chain Y [auth A] SDF format, chain YA [auth S] SDF format, chain MA [auth I] MOL2 format, chain AB [auth U] MOL2 format, chain BB [auth W] MOL2 format, chain CA [auth C] MOL2 format, chain GA [auth E] MOL2 format, chain JA [auth G] MOL2 format, chain NA [auth K] MOL2 format, chain OA [auth M] MOL2 format, chain RA [auth O] MOL2 format, chain VA [auth Q] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth S] MOL2 format, chain MA [auth I] mmCIF format, chain AB [auth U] mmCIF format, chain BB [auth W] mmCIF format, chain CA [auth C] mmCIF format, chain GA [auth E] mmCIF format, chain JA [auth G] mmCIF format, chain NA [auth K] mmCIF format, chain OA [auth M] mmCIF format, chain RA [auth O] mmCIF format, chain VA [auth Q] mmCIF format, chain Y [auth A] mmCIF format, chain YA [auth S] mmCIF format, chain MA [auth I]	AB [auth U] BB [auth W] CA [auth C] GA [auth E] JA [auth G] AB [auth U], BB [auth W], CA [auth C], GA [auth E], JA [auth G], MA [auth I], NA [auth K], OA [auth M], RA [auth O], VA [auth Q], Y [auth A], YA [auth S]	M-CRESOL C₇ H₈ O RLSSMJSEOOYNOY-UHFFFAOYSA-N		Interactions Focus chain AB [auth U] Focus chain BB [auth W] Focus chain CA [auth C] Focus chain GA [auth E] Focus chain JA [auth G] Focus chain MA [auth I] Focus chain NA [auth K] Focus chain OA [auth M] Focus chain RA [auth O] Focus chain VA [auth Q] Focus chain Y [auth A] Focus chain YA [auth S] Interactions & Density Focus chain AB [auth U] Focus chain BB [auth W] Focus chain CA [auth C] Focus chain GA [auth E] Focus chain JA [auth G] Focus chain MA [auth I] Focus chain NA [auth K] Focus chain OA [auth M] Focus chain RA [auth O] Focus chain VA [auth Q] Focus chain Y [auth A] Focus chain YA [auth S]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain SA [auth P] SDF format, chain PA [auth N] SDF format, chain DA [auth D] SDF format, chain AA [auth B] MOL2 format, chain SA [auth P] MOL2 format, chain PA [auth N] MOL2 format, chain DA [auth D] MOL2 format, chain AA [auth B] mmCIF format, chain SA [auth P] mmCIF format, chain PA [auth N] mmCIF format, chain DA [auth D] mmCIF format, chain AA [auth B]	AA [auth B], DA [auth D], PA [auth N], SA [auth P]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain DA [auth D] Focus chain PA [auth N] Focus chain SA [auth P] Interactions & Density Focus chain AA [auth B] Focus chain DA [auth D] Focus chain PA [auth N] Focus chain SA [auth P]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain IA [auth F] SDF format, chain KA [auth H] SDF format, chain LA [auth H] SDF format, chain WA [auth Q] SDF format, chain XA [auth R] SDF format, chain ZA [auth T] SDF format, chain Z [auth A] SDF format, chain TA [auth P] SDF format, chain HA [auth E] SDF format, chain EA [auth D] MOL2 format, chain IA [auth F] MOL2 format, chain KA [auth H] MOL2 format, chain LA [auth H] MOL2 format, chain WA [auth Q] MOL2 format, chain XA [auth R] MOL2 format, chain ZA [auth T] MOL2 format, chain Z [auth A] MOL2 format, chain TA [auth P] MOL2 format, chain HA [auth E] MOL2 format, chain EA [auth D] mmCIF format, chain IA [auth F] mmCIF format, chain KA [auth H] mmCIF format, chain LA [auth H] mmCIF format, chain WA [auth Q] mmCIF format, chain XA [auth R] mmCIF format, chain ZA [auth T] mmCIF format, chain Z [auth A] mmCIF format, chain TA [auth P] mmCIF format, chain HA [auth E] mmCIF format, chain EA [auth D]	EA [auth D] HA [auth E] IA [auth F] KA [auth H] LA [auth H] EA [auth D], HA [auth E], IA [auth F], KA [auth H], LA [auth H], TA [auth P], WA [auth Q], XA [auth R], Z [auth A], ZA [auth T]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain EA [auth D] Focus chain HA [auth E] Focus chain IA [auth F] Focus chain KA [auth H] Focus chain LA [auth H] Focus chain TA [auth P] Focus chain WA [auth Q] Focus chain XA [auth R] Focus chain Z [auth A] Focus chain ZA [auth T] Interactions & Density Focus chain EA [auth D] Focus chain HA [auth E] Focus chain IA [auth F] Focus chain KA [auth H] Focus chain LA [auth H] Focus chain TA [auth P] Focus chain WA [auth Q] Focus chain XA [auth R] Focus chain Z [auth A] Focus chain ZA [auth T]
IS8 Query on IS8 Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain FA [auth D] SDF format, chain QA [auth N] SDF format, chain UA [auth P] MOL2 format, chain BA [auth B] MOL2 format, chain FA [auth D] MOL2 format, chain QA [auth N] MOL2 format, chain UA [auth P] mmCIF format, chain BA [auth B] mmCIF format, chain FA [auth D] mmCIF format, chain QA [auth N] mmCIF format, chain UA [auth P]	BA [auth B], FA [auth D], QA [auth N], UA [auth P]	isothiocyanate C H N S GRHBQAYDJPGGLF-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain FA [auth D] Focus chain QA [auth N] Focus chain UA [auth P] Interactions & Density Focus chain BA [auth B] Focus chain FA [auth D] Focus chain QA [auth N] Focus chain UA [auth P]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.279 (Depositor), 0.276 (DCC)
R-Value Work: 0.223 (Depositor), 0.226 (DCC)
R-Value Observed: 0.226 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.662	α = 90
b = 70.361	β = 105.21
c = 84.748	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-06-12

Deposition Author(s):

Funding Organization	Location	Grant Number
European Union	Greece	BioStruct-X,No.283570
"General Secretariat for Research and Technology (GSRT) - Hellenic Foundation for Research and Innovation	Greece	2467

Revision History (Full details and data files)

Version 1.0: 2019-06-12
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-11-13
Changes: Structure summary