5UU3 | pdb_00005uu3

Insulin with proline analog DfP at position B28 in the R6 state

PDB DOI: https://doi.org/10.2210/pdb5UU3/pdb

Classification: HORMONE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-02-16 Released: 2018-02-21
Deposition Author(s): Lieblich, S.A., Fang, K.Y., Tirrell, D.A.
Funding Organization(s): Novo Nordisk Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.292 (Depositor), 0.298 (DCC)
R-Value Work:
0.243 (Depositor), 0.252 (DCC)
R-Value Observed:
0.246 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Insulin with proline analog DfP at position B28 in the R6 state

Lieblich, S.A., Fang, K.Y., Tirrell, D.A.

To be published.

Macromolecule Content

Total Structure Weight: 71.68 kDa
Atom Count: 4,117
Modeled Residue Count: 572
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, chain B	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, chain A	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IPH Query on IPH Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain FA [auth G] SDF format, chain GA [auth I] SDF format, chain HA [auth K] SDF format, chain IA [auth M] SDF format, chain NA [auth Q] SDF format, chain OA [auth S] SDF format, chain PA [auth U] SDF format, chain QA [auth W] SDF format, chain Y [auth A] SDF format, chain DA [auth E] MOL2 format, chain AA [auth C] MOL2 format, chain FA [auth G] MOL2 format, chain GA [auth I] MOL2 format, chain HA [auth K] MOL2 format, chain IA [auth M] MOL2 format, chain NA [auth Q] MOL2 format, chain OA [auth S] MOL2 format, chain PA [auth U] MOL2 format, chain QA [auth W] MOL2 format, chain Y [auth A] MOL2 format, chain DA [auth E] mmCIF format, chain AA [auth C] mmCIF format, chain FA [auth G] mmCIF format, chain GA [auth I] mmCIF format, chain HA [auth K] mmCIF format, chain IA [auth M] mmCIF format, chain NA [auth Q] mmCIF format, chain OA [auth S] mmCIF format, chain PA [auth U] mmCIF format, chain QA [auth W] mmCIF format, chain Y [auth A] mmCIF format, chain DA [auth E]	AA [auth C] DA [auth E] FA [auth G] GA [auth I] HA [auth K] AA [auth C], DA [auth E], FA [auth G], GA [auth I], HA [auth K], IA [auth M], NA [auth Q], OA [auth S], PA [auth U], QA [auth W], Y [auth A]	PHENOL C₆ H₆ O ISWSIDIOOBJBQZ-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain DA [auth E] Focus chain FA [auth G] Focus chain GA [auth I] Focus chain HA [auth K] Focus chain IA [auth M] Focus chain NA [auth Q] Focus chain OA [auth S] Focus chain PA [auth U] Focus chain QA [auth W] Focus chain Y [auth A] Interactions & Density Focus chain AA [auth C] Focus chain DA [auth E] Focus chain FA [auth G] Focus chain GA [auth I] Focus chain HA [auth K] Focus chain IA [auth M] Focus chain NA [auth Q] Focus chain OA [auth S] Focus chain PA [auth U] Focus chain QA [auth W] Focus chain Y [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain JA [auth N] SDF format, chain LA [auth P] SDF format, chain Z [auth B] SDF format, chain BA [auth D] MOL2 format, chain JA [auth N] MOL2 format, chain LA [auth P] MOL2 format, chain Z [auth B] MOL2 format, chain BA [auth D] mmCIF format, chain JA [auth N] mmCIF format, chain LA [auth P] mmCIF format, chain Z [auth B] mmCIF format, chain BA [auth D]	BA [auth D], JA [auth N], LA [auth P], Z [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain JA [auth N] Focus chain LA [auth P] Focus chain Z [auth B] Interactions & Density Focus chain BA [auth D] Focus chain JA [auth N] Focus chain LA [auth P] Focus chain Z [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain EA [auth F] SDF format, chain KA [auth N] SDF format, chain MA [auth P] SDF format, chain CA [auth D] MOL2 format, chain EA [auth F] MOL2 format, chain KA [auth N] MOL2 format, chain MA [auth P] MOL2 format, chain CA [auth D] mmCIF format, chain EA [auth F] mmCIF format, chain KA [auth N] mmCIF format, chain MA [auth P] mmCIF format, chain CA [auth D]	CA [auth D], EA [auth F], KA [auth N], MA [auth P]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain CA [auth D] Focus chain EA [auth F] Focus chain KA [auth N] Focus chain MA [auth P] Interactions & Density Focus chain CA [auth D] Focus chain EA [auth F] Focus chain KA [auth N] Focus chain MA [auth P]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.292 (Depositor), 0.298 (DCC)
R-Value Work: 0.243 (Depositor), 0.252 (DCC)
R-Value Observed: 0.246 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.599	α = 89.96
b = 47.425	β = 89.93
c = 78.705	γ = 73.41

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2018-02-21

Deposition Author(s):

Lieblich, S.A.

Fang, K.Y.

Tirrell, D.A.

Funding Organization	Location	Grant Number
Novo Nordisk Foundation	Denmark	--

Revision History (Full details and data files)

Version 1.0: 2018-02-21
Type: Initial release
Version 1.1: 2020-01-15
Changes: Author supporting evidence
Version 1.2: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2023-11-15
Changes: Data collection, Derived calculations