3IR0 | pdb_00003ir0

Crystal Structure of Human Insulin complexed with Cu+2 metal ion

PDB DOI: https://doi.org/10.2210/pdb3IR0/pdb

Classification: HORMONE
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2009-08-21 Released: 2010-09-01
Deposition Author(s): Raghavendra, N., Pattabhi, V., Rajan, S.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.299 (Depositor), 0.324 (DCC)
R-Value Work:
0.268 (Depositor), 0.301 (DCC)
R-Value Observed:
0.269 (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

Metal induced structural changes observed in Human insulin

Raghavendra, N., Pattabhi, V., Rajan, S.S.

To be published.

Macromolecule Content

Total Structure Weight: 70.57 kDa
Atom Count: 5,143
Modeled Residue Count: 612
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 chain	A C E G I A, C, E, G, I, K, M, O, Q [auth R], S [auth T], U [auth V], W [auth X]	21	Homo sapiens	Mutation(s): 0
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 chain	B D F H J B, D, F, H, J, L, N, P, R [auth S], T [auth U], V [auth W], X [auth Y]	30	Homo sapiens	Mutation(s): 0
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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain BA [auth H] SDF format, chain CA [auth J] SDF format, chain DA [auth L] SDF format, chain GA [auth S] SDF format, chain HA [auth U] SDF format, chain IA [auth W] SDF format, chain JA [auth Y] SDF format, chain Z [auth D] SDF format, chain Y [auth B] SDF format, chain FA [auth P] SDF format, chain EA [auth N] MOL2 format, chain AA [auth F] MOL2 format, chain BA [auth H] MOL2 format, chain CA [auth J] MOL2 format, chain DA [auth L] MOL2 format, chain GA [auth S] MOL2 format, chain HA [auth U] MOL2 format, chain IA [auth W] MOL2 format, chain JA [auth Y] MOL2 format, chain Z [auth D] MOL2 format, chain Y [auth B] MOL2 format, chain FA [auth P] MOL2 format, chain EA [auth N] mmCIF format, chain AA [auth F] mmCIF format, chain BA [auth H] mmCIF format, chain CA [auth J] mmCIF format, chain DA [auth L] mmCIF format, chain GA [auth S] mmCIF format, chain HA [auth U] mmCIF format, chain IA [auth W] mmCIF format, chain JA [auth Y] mmCIF format, chain Z [auth D] mmCIF format, chain Y [auth B] mmCIF format, chain FA [auth P] mmCIF format, chain EA [auth N]	AA [auth F] BA [auth H] CA [auth J] DA [auth L] EA [auth N] AA [auth F], BA [auth H], CA [auth J], DA [auth L], EA [auth N], FA [auth P], GA [auth S], HA [auth U], IA [auth W], JA [auth Y], Y [auth B], Z [auth D]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain BA [auth H] Focus chain CA [auth J] Focus chain DA [auth L] Focus chain EA [auth N] Focus chain FA [auth P] Focus chain GA [auth S] Focus chain HA [auth U] Focus chain IA [auth W] Focus chain JA [auth Y] Focus chain Y [auth B] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth F] Focus chain BA [auth H] Focus chain CA [auth J] Focus chain DA [auth L] Focus chain EA [auth N] Focus chain FA [auth P] Focus chain GA [auth S] Focus chain HA [auth U] Focus chain IA [auth W] Focus chain JA [auth Y] Focus chain Y [auth B] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.299 (Depositor), 0.324 (DCC)
R-Value Work: 0.268 (Depositor), 0.301 (DCC)
R-Value Observed: 0.269 (Depositor)

Space Group: P 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.559	α = 90
b = 81.559	β = 90
c = 68.825	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
AMoRE	phasing
REFMAC	refinement
AUTOMAR	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-09-01

Deposition Author(s):

Raghavendra, N.

Pattabhi, V.

Rajan, S.S.

Revision History (Full details and data files)

Version 1.0: 2010-09-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-10-30
Changes: Structure summary

3IR0 | pdb_00003ir0

Crystal Structure of Human Insulin complexed with Cu+2 metal ion

Literature

Metal induced structural changes observed in Human insulin

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Biological Assembly 4

Biological Assembly 5

Biological Assembly 6

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2