SAXSdb — 6h0f

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Protein cereblon

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1 × 1 DNA-binding protein Ikaros × 1 （Q13422） ZINC ION × 2 S-Pomalidomide × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1 × 1 DNA-binding protein Ikaros × 1 （Q13422） ZINC ION × 2 S-Pomalidomide × 1 water × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1 × 1 DNA-binding protein Ikaros × 1 （Q13422） ZINC ION × 2 S-Pomalidomide × 1 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 3	DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1 × 1 DNA-binding protein Ikaros × 1 （Q13422） ZINC ION × 2 S-Pomalidomide × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CRBN_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 20–426； UniProt 36–442 Author chain E； PDBConstruct 20–426； UniProt 36–442 Author chain H； PDBConstruct 20–426； UniProt 36–442 Author chain K； PDBConstruct 20–426； UniProt 36–442

DNA-binding protein Ikaros

Homo sapiens

UniProt Q13422

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1 × 1 Protein cereblon × 1 （Q96SW2） ZINC ION × 2 S-Pomalidomide × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1 × 1 Protein cereblon × 1 （Q96SW2） ZINC ION × 2 S-Pomalidomide × 1 water × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1 × 1 Protein cereblon × 1 （Q96SW2） ZINC ION × 2 S-Pomalidomide × 1 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 3	DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1 × 1 Protein cereblon × 1 （Q96SW2） ZINC ION × 2 S-Pomalidomide × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IKZF1_HUMAN
Isoform	Q13422-4
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 5–38； UniProt 97–130 Author chain F； PDBConstruct 5–38； UniProt 97–130 Author chain I； PDBConstruct 5–38； UniProt 97–130 Author chain L； PDBConstruct 5–38； UniProt 97–130

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6h0f
Deposition date deposition_date	2018-07-09
Structure title title	Structure of DDB1-CRBN-pomalidomide complex bound to IKZF1(ZF2)
Keywords keywords	E3 ubiquitin ligase, drug mediated protein-interaction, targeted protein degradation, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

6h0f__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6h0f__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6h0f__assembly_4__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	35.82 Å
Rg (electron density)	34.97 Å
Total Rg	35.48 Å
Atom count	19570
Residues	1249
Excluded volume	175430 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6h0f__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6h0f__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6h0f__assembly_3__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`6h0f__assembly_4__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1
Molecular weight formula_weight	95773.7 kDa
Mutation mutation	;Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG) ;
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D,G,J
Atom count atom_count	77598

MHHHHHHVDEENLYFQGGGRMSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGKIAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGIIGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICFVYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYHNGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGGNGNSGEIQKLHIRTVPLYESPRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHETSFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEEAEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELRTECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGETSTPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTERKTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Trichoplusia ni cypovirus 15

Entity 2 Entity 2 polymer

Description description	Protein cereblon
Molecular weight formula_weight	48976.1 kDa
Mutation mutation	N-terminally truncated (1-40 aa deleted)
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E,H,K

MDWSHPQFEKSAVDENLYFQGGGRAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPDKVILCL

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Trichoplusia ni

Entity 3 Entity 3 polymer

Description description	DNA-binding protein Ikaros
Molecular weight formula_weight	4193.8 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F,I,L

GGGRGERPFQCNQCGASFTQKGNLLRHIKLHSGEKPFK

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Trichoplusia ni

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	man
Copy count entity_count	8

Entity 5 Entity 5 non-polymer

Description description	S-Pomalidomide
Molecular weight formula_weight	273.2 kDa
Source method src_method	man
Copy count entity_count	4

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	32

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6. Fold Classification (SCOP + CATH) 7 domains

CATH v4.4 (7 domains)

Domain ID domain_id	6h0fA01
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	6h0fA02
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	6h0fG01
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	6h0fG02
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	6h0fJ01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	910 —

Domain ID domain_id	6h0fJ02
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	6h0fJ03
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

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Unit-cell length a length_a	161.450 Å
Unit-cell length b length_b	177.860 Å
Unit-cell length c length_c	242.470 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.250 Å
Low-resolution limit resolution_low	39.850 Å
R factor r_factor	0.2130
R_work r_work	0.2120
R_free r_free	0.2340

Structure of DDB1-CRBN-pomalidomide complex bound to IKZF1(ZF2)

1. Protein Identity and Related Structures Protein Identity & Related Structures

Protein cereblon

State in the Current Structure

Other States of the Same Protein in the Database

DNA-binding protein Ikaros

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6h0f__assembly_4__model_1

6h0f__assembly_4__model_1 | I(q)

6h0f__assembly_4__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 7 domains

CATH v4.4 (7 domains)

7. Citations (1)

Structure of DDB1-CRBN-pomalidomide complex bound to IKZF1(ZF2)

1. Protein Identity and Related Structures Protein Identity & Related Structures

Protein cereblon

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA-binding protein Ikaros

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6h0f__assembly_4__model_1

6h0f__assembly_4__model_1 | I(q)

6h0f__assembly_4__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 7 domains

CATH v4.4 (7 domains)

7. Citations (1)