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), 0.280 (DCC)
R-Value Work:
0.223 (Depositor), 0.230 (DCC)
R-Value Observed:
0.226 (Depositor)

Starting Model: experimental
View more details

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% 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, 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% 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 YA [auth S] SDF format, chain Y [auth A] SDF format, chain VA [auth Q] SDF format, chain RA [auth O] SDF format, chain OA [auth M] SDF format, chain NA [auth K] SDF format, chain MA [auth I] SDF format, chain JA [auth G] SDF format, chain GA [auth E] SDF format, chain CA [auth C] SDF format, chain BB [auth W] SDF format, chain AB [auth U] MOL2 format, chain YA [auth S] MOL2 format, chain Y [auth A] MOL2 format, chain VA [auth Q] MOL2 format, chain RA [auth O] MOL2 format, chain OA [auth M] MOL2 format, chain NA [auth K] MOL2 format, chain MA [auth I] MOL2 format, chain JA [auth G] MOL2 format, chain GA [auth E] MOL2 format, chain CA [auth C] MOL2 format, chain BB [auth W] MOL2 format, chain AB [auth U] mmCIF format, chain YA [auth S] mmCIF format, chain Y [auth A] mmCIF format, chain VA [auth Q] mmCIF format, chain RA [auth O] mmCIF format, chain OA [auth M] mmCIF format, chain NA [auth K] mmCIF format, chain MA [auth I] mmCIF format, chain JA [auth G] mmCIF format, chain GA [auth E] mmCIF format, chain CA [auth C] mmCIF format, chain BB [auth W] mmCIF format, chain AB [auth U]	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 ZA [auth T] SDF format, chain Z [auth A] SDF format, chain XA [auth R] SDF format, chain WA [auth Q] SDF format, chain TA [auth P] SDF format, chain LA [auth H] SDF format, chain KA [auth H] SDF format, chain IA [auth F] SDF format, chain HA [auth E] SDF format, chain EA [auth D] MOL2 format, chain ZA [auth T] MOL2 format, chain Z [auth A] MOL2 format, chain XA [auth R] MOL2 format, chain WA [auth Q] MOL2 format, chain TA [auth P] MOL2 format, chain LA [auth H] MOL2 format, chain KA [auth H] MOL2 format, chain IA [auth F] MOL2 format, chain HA [auth E] MOL2 format, chain EA [auth D] mmCIF format, chain ZA [auth T] mmCIF format, chain Z [auth A] mmCIF format, chain XA [auth R] mmCIF format, chain WA [auth Q] mmCIF format, chain TA [auth P] mmCIF format, chain LA [auth H] mmCIF format, chain KA [auth H] mmCIF format, chain IA [auth F] 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 UA [auth P] SDF format, chain QA [auth N] SDF format, chain FA [auth D] SDF format, chain BA [auth B] MOL2 format, chain UA [auth P] MOL2 format, chain QA [auth N] MOL2 format, chain FA [auth D] MOL2 format, chain BA [auth B] mmCIF format, chain UA [auth P] mmCIF format, chain QA [auth N] mmCIF format, chain FA [auth D] mmCIF format, chain BA [auth B]	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), 0.280 (DCC)
R-Value Work: 0.223 (Depositor), 0.230 (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

View Full Validation Report

Ligand Structure Quality Assessment

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