11LZ | pdb_000011lz

Crystal structure of Interferon alpha2 bound to IFA001 Fab

PDB DOI: https://doi.org/10.2210/pdb11LZ/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2026-03-04 Released: 2026-11-04
Deposition Author(s): Vasquez, S., Rubio, A.A., Barnes, C.O.
Funding Organization(s): Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.279 (Depositor), 0.278 (DCC)
R-Value Work:
0.221 (Depositor), 0.221 (DCC)
R-Value Observed:
0.225 (Depositor)

Starting Models: experimental
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Ligand Structure Quality Assessment

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Literature

Developmental and molecular features shaping broad and synergistic actions of human autoantibodies targeting IFN alpha

Groen, K., Moritz, J.A., Vasquez, S., Rubio, A.A., Kuratli, R., Jones, D., Grafl, D., Motta, M., Fontana, S., Manning, J., Costagli, S., Simonelli, L., Thakur, R., Jarrossay, D., Tran, C., Lee, Y.E., Abela, I.A., Calmy, A., Hirzel, C., Kaufmann, D.E., Swiss HIV Cohort Study, Gunthard, H.F., Kouyos, R.D., Barnes, C.O., Robbiani, D.F., Hale, B.G.

(2026) bioRxiv

DOI: https://doi.org/10.64898/2026.10.20.760426

Macromolecule Content

Total Structure Weight: 140.39 kDa
Atom Count: 8,531
Modeled Residue Count: 1,112
Deposited Residue Count: 1,280
Unique protein chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interferon alpha-2	A, B	194	Homo sapiens	Mutation(s): 0 Gene Names: IFNA2, IFNA2A, IFNA2B, IFNA2C
UniProt & NIH Common Fund Data Resources
Find proteins for P01563 (Homo sapiens) Explore P01563 Go to UniProtKB: P01563
PHAROS: P01563 GTEx: ENSG00000188379
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01563
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
IFA001 Fab light chain	C, F [auth L]	216	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
IFA001 Fab heavy chain	D, E [auth H]	230	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain D Focus chain E [auth H]
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 G [auth D] SDF format, chain H MOL2 format, chain G [auth D] MOL2 format, chain H mmCIF format, chain G [auth D] mmCIF format, chain H	G [auth D], H	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth D] Focus chain H Interactions & Density Focus chain G [auth D] Focus chain H

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.279 (Depositor), 0.278 (DCC)
R-Value Work: 0.221 (Depositor), 0.221 (DCC)
R-Value Observed: 0.225 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.732	α = 100.202
b = 63.444	β = 97.261
c = 130.26	γ = 91.06

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-11-04

Deposition Author(s):

Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History (Full details and data files)

Version 1.0: 2026-11-04
Type: Initial release