5UQA | pdb_00005uqa

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

PDB DOI: https://doi.org/10.2210/pdb5UQA/pdb

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

Deposited: 2017-02-07 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: 1.31 Å
R-Value Free:
0.182 (Depositor), 0.180 (DCC)
R-Value Work:
0.152 (Depositor), 0.150 (DCC)
R-Value Observed:
0.154 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

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

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

To be published.

Macromolecule Content

Total Structure Weight: 36.07 kDa
Atom Count: 2,688
Modeled Residue Count: 297
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, chain A	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% 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, chain B	B, D, F, H, J B, D, F, H, J, L	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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IPH Query on IPH Download Ideal Coordinates CCD File SDF format, chain BA [auth K] SDF format, chain M [auth A] SDF format, chain P [auth C] SDF format, chain R [auth E] SDF format, chain V [auth G] SDF format, chain X [auth I] MOL2 format, chain BA [auth K] MOL2 format, chain M [auth A] MOL2 format, chain P [auth C] MOL2 format, chain R [auth E] MOL2 format, chain V [auth G] MOL2 format, chain X [auth I] mmCIF format, chain BA [auth K] mmCIF format, chain M [auth A] mmCIF format, chain P [auth C] mmCIF format, chain R [auth E] mmCIF format, chain V [auth G] mmCIF format, chain X [auth I]	BA [auth K] M [auth A] P [auth C] R [auth E] V [auth G] BA [auth K], M [auth A], P [auth C], R [auth E], V [auth G], X [auth I]	PHENOL C₆ H₆ O ISWSIDIOOBJBQZ-UHFFFAOYSA-N		Interactions Focus chain BA [auth K] Focus chain M [auth A] Focus chain P [auth C] Focus chain R [auth E] Focus chain V [auth G] Focus chain X [auth I] Interactions & Density Focus chain BA [auth K] Focus chain M [auth A] Focus chain P [auth C] Focus chain R [auth E] Focus chain V [auth G] Focus chain X [auth I]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth J] MOL2 format, chain AA [auth J] mmCIF format, chain AA [auth J]	AA [auth J]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth J] Interactions & Density Focus chain AA [auth J]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain Q [auth D] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth D] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth D]	N [auth B], Q [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Focus chain Q [auth D] Interactions & Density Focus chain N [auth B] Focus chain Q [auth D]
ACN Query on ACN Download Ideal Coordinates CCD File SDF format, chain DA [auth L] MOL2 format, chain DA [auth L] mmCIF format, chain DA [auth L]	DA [auth L]	ACETONE C₃ H₆ O CSCPPACGZOOCGX-UHFFFAOYSA-N		Interactions Focus chain DA [auth L] Interactions & Density Focus chain DA [auth L]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain W [auth H] MOL2 format, chain O [auth B] MOL2 format, chain W [auth H] mmCIF format, chain O [auth B] mmCIF format, chain W [auth H]	O [auth B], W [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain O [auth B] Focus chain W [auth H] Interactions & Density Focus chain O [auth B] Focus chain W [auth H]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain CA [auth K] SDF format, chain S [auth E] SDF format, chain T [auth F] SDF format, chain U [auth F] SDF format, chain Y [auth I] SDF format, chain Z [auth J] MOL2 format, chain CA [auth K] MOL2 format, chain S [auth E] MOL2 format, chain T [auth F] MOL2 format, chain U [auth F] MOL2 format, chain Y [auth I] MOL2 format, chain Z [auth J] mmCIF format, chain CA [auth K] mmCIF format, chain S [auth E] mmCIF format, chain T [auth F] mmCIF format, chain U [auth F] mmCIF format, chain Y [auth I] mmCIF format, chain Z [auth J]	CA [auth K] S [auth E] T [auth F] U [auth F] Y [auth I] CA [auth K], S [auth E], T [auth F], U [auth F], Y [auth I], Z [auth J]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain CA [auth K] Focus chain S [auth E] Focus chain T [auth F] Focus chain U [auth F] Focus chain Y [auth I] Focus chain Z [auth J] Interactions & Density Focus chain CA [auth K] Focus chain S [auth E] Focus chain T [auth F] Focus chain U [auth F] Focus chain Y [auth I] Focus chain Z [auth J]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
4FB Query on 4FB	B, D, F, H, J B, D, F, H, J, L	L-PEPTIDE LINKING	C₅ H₈ F N O₂		PRO

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.31 Å
R-Value Free: 0.182 (Depositor), 0.180 (DCC)
R-Value Work: 0.152 (Depositor), 0.150 (DCC)
R-Value Observed: 0.154 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.936	α = 90
b = 61.258	β = 111.694
c = 60.39	γ = 90

Software Package:

Software Name	Purpose
phenix.refine	refinement
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

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
Version 1.4: 2024-10-30
Changes: Structure summary