6NWV | pdb_00006nwv

Insulin Lispro Analog

PDB DOI: https://doi.org/10.2210/pdb6NWV/pdb

Classification: HORMONE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2019-02-07 Released: 2020-02-12
Deposition Author(s): Cruz-Rangel, A., Romero, A., Reyes-Grajeda, J.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.257 (Depositor), 0.259 (DCC)
R-Value Work:
0.208 (Depositor), 0.216 (DCC)
R-Value Observed:
0.213 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of Lispro hexameric insulin analog

Cruz-Rangel, A., Romero, A., Reyes-Grajeda, J.P.

To be published.

Macromolecule Content

Total Structure Weight: 36.05 kDa
Atom Count: 2,542
Modeled Residue Count: 300
Deposited Residue Count: 306
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, E, G, I A, C, E, G, I, K	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 Lispro B chain	B, D, F, H, J B, D, F, H, J, L	30	Homo sapiens	Mutation(s): 2 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 Query on CRS Download:Ideal Coordinates CCD File SDF format, chain Q [auth E] SDF format, chain U [auth G] SDF format, chain V [auth I] SDF format, chain X [auth K] SDF format, chain T [auth G] SDF format, chain O [auth C] SDF format, chain M [auth A] MOL2 format, chain Q [auth E] MOL2 format, chain U [auth G] MOL2 format, chain V [auth I] MOL2 format, chain X [auth K] MOL2 format, chain T [auth G] MOL2 format, chain O [auth C] MOL2 format, chain M [auth A] mmCIF format, chain Q [auth E] mmCIF format, chain U [auth G] mmCIF format, chain V [auth I] mmCIF format, chain X [auth K] mmCIF format, chain T [auth G] mmCIF format, chain O [auth C] mmCIF format, chain M [auth A]	M [auth A] O [auth C] Q [auth E] T [auth G] U [auth G] M [auth A], O [auth C], Q [auth E], T [auth G], U [auth G], V [auth I], X [auth K]	M-CRESOL C₇ H₈ O RLSSMJSEOOYNOY-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain O [auth C] Focus chain Q [auth E] Focus chain T [auth G] Focus chain U [auth G] Focus chain V [auth I] Focus chain X [auth K] Interactions & Density Focus chain M [auth A] Focus chain O [auth C] Focus chain Q [auth E] Focus chain T [auth G] Focus chain U [auth G] Focus chain V [auth I] Focus chain X [auth K]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain S [auth F] SDF format, chain P [auth D] MOL2 format, chain S [auth F] MOL2 format, chain P [auth D] mmCIF format, chain S [auth F] mmCIF format, chain P [auth D]	P [auth D], S [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain P [auth D] Focus chain S [auth F] Interactions & Density Focus chain P [auth D] Focus chain S [auth F]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain R [auth F] MOL2 format, chain N [auth B] MOL2 format, chain R [auth F] mmCIF format, chain N [auth B] mmCIF format, chain R [auth F]	N [auth B], R [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Focus chain R [auth F] Interactions & Density Focus chain N [auth B] Focus chain R [auth F]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain Y [auth L] SDF format, chain W [auth J] MOL2 format, chain Y [auth L] MOL2 format, chain W [auth J] mmCIF format, chain Y [auth L] mmCIF format, chain W [auth J]	W [auth J], Y [auth L]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain W [auth J] Focus chain Y [auth L] Interactions & Density Focus chain W [auth J] Focus chain Y [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.257 (Depositor), 0.259 (DCC)
R-Value Work: 0.208 (Depositor), 0.216 (DCC)
R-Value Observed: 0.213 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.161	α = 90
b = 61.789	β = 111.46
c = 58.618	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2020-02-12

Deposition Author(s):

Cruz-Rangel, A.

Romero, A.

Reyes-Grajeda, J.P.

Revision History (Full details and data files)

Version 1.0: 2020-02-12
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-11-13
Changes: Structure summary

6NWV | pdb_00006nwv

Insulin Lispro Analog

Literature

Crystal structure of Lispro hexameric insulin analog

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 2