3QAZ

IL-2 mutant D10 ternary complex

PDB DOI: https://doi.org/10.2210/pdb3QAZ/pdb

Classification: SIGNALING PROTEIN/Cytokine
Organism(s): Homo sapiens
Expression System: Trichoplusia ni
Mutation(s): Yes

Deposited: 2011-01-12 Released: 2012-04-11
Deposition Author(s): Levin, A.M., Bates, D.L., Ring, A.M., Lin, J.T., Su, L., Krieg, C., Bowman, G.R., Novick, P., Pande, V.S., Khort, H.E., Boyman, O., Gathman, C.G., Garcia, K.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.80 Å
R-Value Free: 0.344
R-Value Work: 0.291
R-Value Observed: 0.292

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Macromolecule Content

Total Structure Weight: 791.56 kDa
Atom Count: 51,562
Modelled Residue Count: 6,076
Deposited Residue Count: 6,660
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-2	A BA [auth b] D EA [auth e] G A, BA [auth b], D, EA [auth e], G, HA [auth h], J, M, P, S, V, Y	136	Homo sapiens	Mutation(s): 6 Gene Names: IL2
UniProt & NIH Common Fund Data Resources
Find proteins for P60568 (Homo sapiens) Explore P60568 Go to UniProtKB: P60568
PHAROS: P60568 GTEx: ENSG00000109471
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P60568
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-2 receptor subunit beta	B CA [auth c] E FA [auth f] H B, CA [auth c], E, FA [auth f], H, IA [auth i], K, N, Q, T, W, Z	217	Homo sapiens	Mutation(s): 5 Gene Names: IL2RB
UniProt & NIH Common Fund Data Resources
Find proteins for P14784 (Homo sapiens) Explore P14784 Go to UniProtKB: P14784
PHAROS: P14784 GTEx: ENSG00000100385
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P14784
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytokine receptor common subunit gamma	AA [auth a] C DA [auth d] F GA [auth g] AA [auth a], C, DA [auth d], F, GA [auth g], I, JA [auth j], L, O, R, U, X	202	Homo sapiens	Mutation(s): 1 Gene Names: IL2RG
UniProt & NIH Common Fund Data Resources
Find proteins for P31785 (Homo sapiens) Explore P31785 Go to UniProtKB: P31785
PHAROS: P31785 GTEx: ENSG00000147168
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P31785
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AC [auth Z] SDF format, chain CC [auth a] SDF format, chain DB [auth K] SDF format, chain DC [auth c] SDF format, chain EB [auth L] SDF format, chain EC [auth c] SDF format, chain FB [auth L] SDF format, chain GB [auth L] SDF format, chain GC [auth f] SDF format, chain HB [auth L] SDF format, chain HC [auth g] SDF format, chain JB [auth O] SDF format, chain JC [auth i] SDF format, chain KA [auth B] SDF format, chain KB [auth O] SDF format, chain KC [auth i] SDF format, chain LC [auth j] SDF format, chain MA [auth C] SDF format, chain NB [auth O] SDF format, chain OA [auth C] SDF format, chain PA [auth C] SDF format, chain PB [auth R] SDF format, chain QA [auth E] SDF format, chain RA [auth F] SDF format, chain SA [auth F] SDF format, chain SB [auth R] SDF format, chain UA [auth F] SDF format, chain UB [auth T] SDF format, chain XA [auth I] SDF format, chain XB [auth W] SDF format, chain YB [auth X] SDF format, chain AB [auth I] SDF format, chain BB [auth I] SDF format, chain BC [auth a] SDF format, chain CB [auth K] SDF format, chain FC [auth d] SDF format, chain IB [auth N] SDF format, chain IC [auth g] SDF format, chain LA [auth C] SDF format, chain LB [auth O] SDF format, chain MB [auth O] SDF format, chain NA [auth C] SDF format, chain OB [auth Q] SDF format, chain QB [auth R] SDF format, chain RB [auth R] SDF format, chain TA [auth F] SDF format, chain TB [auth R] SDF format, chain VA [auth F] SDF format, chain VB [auth U] SDF format, chain WA [auth H] SDF format, chain WB [auth U] SDF format, chain YA [auth I] SDF format, chain ZA [auth I] SDF format, chain ZB [auth X] MOL2 format, chain AC [auth Z] MOL2 format, chain CC [auth a] MOL2 format, chain DB [auth K] MOL2 format, chain DC [auth c] MOL2 format, chain EB [auth L] MOL2 format, chain EC [auth c] MOL2 format, chain FB [auth L] MOL2 format, chain GB [auth L] MOL2 format, chain GC [auth f] MOL2 format, chain HB [auth L] MOL2 format, chain HC [auth g] MOL2 format, chain JB [auth O] MOL2 format, chain JC [auth i] MOL2 format, chain KA [auth B] MOL2 format, chain KB [auth O] MOL2 format, chain KC [auth i] MOL2 format, chain LC [auth j] MOL2 format, chain MA [auth C] MOL2 format, chain NB [auth O] MOL2 format, chain OA [auth C] MOL2 format, chain PA [auth C] MOL2 format, chain PB [auth R] MOL2 format, chain QA [auth E] MOL2 format, chain RA [auth F] MOL2 format, chain SA [auth F] MOL2 format, chain SB [auth R] MOL2 format, chain UA [auth F] MOL2 format, chain UB [auth T] MOL2 format, chain XA [auth I] MOL2 format, chain XB [auth W] MOL2 format, chain YB [auth X] MOL2 format, chain AB [auth I] MOL2 format, chain BB [auth I] MOL2 format, chain BC [auth a] MOL2 format, chain CB [auth K] MOL2 format, chain FC [auth d] MOL2 format, chain IB [auth N] MOL2 format, chain IC [auth g] MOL2 format, chain LA [auth C] MOL2 format, chain LB [auth O] MOL2 format, chain MB [auth O] MOL2 format, chain NA [auth C] MOL2 format, chain OB [auth Q] MOL2 format, chain QB [auth R] MOL2 format, chain RB [auth R] MOL2 format, chain TA [auth F] MOL2 format, chain TB [auth R] MOL2 format, chain VA [auth F] MOL2 format, chain VB [auth U] MOL2 format, chain WA [auth H] MOL2 format, chain WB [auth U] MOL2 format, chain YA [auth I] MOL2 format, chain ZA [auth I] MOL2 format, chain ZB [auth X]	AB [auth I] AC [auth Z] BB [auth I] BC [auth a] CB [auth K] AB [auth I], AC [auth Z], BB [auth I], BC [auth a], CB [auth K], CC [auth a], DB [auth K], DC [auth c], EB [auth L], EC [auth c], FB [auth L], FC [auth d], GB [auth L], GC [auth f], HB [auth L], HC [auth g], IB [auth N], IC [auth g], JB [auth O], JC [auth i], KA [auth B], KB [auth O], KC [auth i], LA [auth C], LB [auth O], LC [auth j], MA [auth C], MB [auth O], NA [auth C], NB [auth O], OA [auth C], OB [auth Q], PA [auth C], PB [auth R], QA [auth E], QB [auth R], RA [auth F], RB [auth R], SA [auth F], SB [auth R], TA [auth F], TB [auth R], UA [auth F], UB [auth T], VA [auth F], VB [auth U], WA [auth H], WB [auth U], XA [auth I], XB [auth W], YA [auth I], YB [auth X], ZA [auth I], ZB [auth X]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth I] Focus chain AC [auth Z] Focus chain BB [auth I] Focus chain BC [auth a] Focus chain CB [auth K] Focus chain CC [auth a] Focus chain DB [auth K] Focus chain DC [auth c] Focus chain EB [auth L] Focus chain EC [auth c] Focus chain FB [auth L] Focus chain FC [auth d] Focus chain GB [auth L] Focus chain GC [auth f] Focus chain HB [auth L] Focus chain HC [auth g] Focus chain IB [auth N] Focus chain IC [auth g] Focus chain JB [auth O] Focus chain JC [auth i] Focus chain KA [auth B] Focus chain KB [auth O] Focus chain KC [auth i] Focus chain LA [auth C] Focus chain LB [auth O] Focus chain LC [auth j] Focus chain MA [auth C] Focus chain MB [auth O] Focus chain NA [auth C] Focus chain NB [auth O] Focus chain OA [auth C] Focus chain OB [auth Q] Focus chain PA [auth C] Focus chain PB [auth R] Focus chain QA [auth E] Focus chain QB [auth R] Focus chain RA [auth F] Focus chain RB [auth R] Focus chain SA [auth F] Focus chain SB [auth R] Focus chain TA [auth F] Focus chain TB [auth R] Focus chain UA [auth F] Focus chain UB [auth T] Focus chain VA [auth F] Focus chain VB [auth U] Focus chain WA [auth H] Focus chain WB [auth U] Focus chain XA [auth I] Focus chain XB [auth W] Focus chain YA [auth I] Focus chain YB [auth X] Focus chain ZA [auth I] Focus chain ZB [auth X] Interactions & Density Focus chain AB [auth I] Focus chain AC [auth Z] Focus chain BB [auth I] Focus chain BC [auth a] Focus chain CB [auth K] Focus chain CC [auth a] Focus chain DB [auth K] Focus chain DC [auth c] Focus chain EB [auth L] Focus chain EC [auth c] Focus chain FB [auth L] Focus chain FC [auth d] Focus chain GB [auth L] Focus chain GC [auth f] Focus chain HB [auth L] Focus chain HC [auth g] Focus chain IB [auth N] Focus chain IC [auth g] Focus chain JB [auth O] Focus chain JC [auth i] Focus chain KA [auth B] Focus chain KB [auth O] Focus chain KC [auth i] Focus chain LA [auth C] Focus chain LB [auth O] Focus chain LC [auth j] Focus chain MA [auth C] Focus chain MB [auth O] Focus chain NA [auth C] Focus chain NB [auth O] Focus chain OA [auth C] Focus chain OB [auth Q] Focus chain PA [auth C] Focus chain PB [auth R] Focus chain QA [auth E] Focus chain QB [auth R] Focus chain RA [auth F] Focus chain RB [auth R] Focus chain SA [auth F] Focus chain SB [auth R] Focus chain TA [auth F] Focus chain TB [auth R] Focus chain UA [auth F] Focus chain UB [auth T] Focus chain VA [auth F] Focus chain VB [auth U] Focus chain WA [auth H] Focus chain WB [auth U] Focus chain XA [auth I] Focus chain XB [auth W] Focus chain YA [auth I] Focus chain YB [auth X] Focus chain ZA [auth I] Focus chain ZB [auth X]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.80 Å
R-Value Free: 0.344
R-Value Work: 0.291
R-Value Observed: 0.292
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.226	α = 99.86
b = 118.099	β = 99.86
c = 236.115	γ = 99.74

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-04-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-04-11
Type: Initial release
Version 1.1: 2014-10-15
Changes: Structure summary
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary