9OTY: DNA damage-binding protein 1

Name: PDB 9OTY: DDB1-CRBN with CK1 alpha, SB-405483, and DEG-47: composite map and model submission
Published: 2025-11-19
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

DDB1-CRBN with CK1 alpha, SB-405483, and DEG-47: composite map and model submission. Determined by electron microscopy at 3.0 Å resolution. Released 19 Nov 2025.

Method: Electron microscopy
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 3
Atoms: 11,542
Mol. weight: 172.51 kDa
Ligands: ZN, A1CEH, A1CEG
Released: 19 Nov 2025

Explore 9OTY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9OTY contains 49 α-helices and 104 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 15 helices, 68 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	1
β-strand	15-21	7	2
β-strand	30-35	6	2
β-strand	38-44	7	2
β-strand	49-56	8	2
β-strand	61-67	7	3
β-strand	76-81	6	3
β-strand	85-94	10	3
β-strand	97-107	11	3
α-helix	114	1
β-strand	115	1	4
α-helix	116	1
β-strand	121-124	4	5
β-strand	130-134	5	5
β-strand	136	1	4
β-strand	139-144	6	5
β-strand	155-158	4	5
β-strand	163-169	7	6
α-helix	170	1
β-strand	177-183	7	6
β-strand	188-196	9	6
β-strand	201-204	4	6
β-strand	209	1	6
β-strand	216-221	6	7
β-strand	229-233	5	7
β-strand	237-241	5	7
β-strand	244-248	5	7
α-helix	251-253	3
β-strand	258-263	6	8
β-strand	270-275	6	8
β-strand	279-287	9	8
β-strand	297-307	11	8
β-strand	311-316	6	9
β-strand	321-326	6	9
β-strand	331-336	6	9
β-strand	347-353	7	9
β-strand	359-365	7	10
β-strand	374-379	6	10
α-helix	382-384	3
β-strand	386-390	5	10
β-strand	712-716	5	10
β-strand	720-727	8	11
β-strand	732-743	12	11
β-strand	749-751	3	11
β-strand	762-765	4	11
β-strand	785-795	11	11
β-strand	801-806	6	11
β-strand	811-819	9	12
β-strand	828-835	8	12
β-strand	846-854	9	12
β-strand	857-866	10	12
β-strand	870-876	7	13
β-strand	879-884	6	13
β-strand	887-893	7	13
β-strand	899-905	7	13
β-strand	913-917	5	14
β-strand	920-924	5	14
β-strand	929-936	8	14
β-strand	941-949	9	14
β-strand	957-959	3	15
β-strand	964-969	6	15
β-strand	973-978	6	15
α-helix	986-989	4
β-strand	991	1	14
β-strand	993-999	7	15
β-strand	1004-1008	5	1
β-strand	1025-1032	8	1
β-strand	1037-1042	6	1
α-helix	1045-1059	15
α-helix	1063-1064	2
α-helix	1070-1073	4
β-strand	1076-1077	2	16
β-strand	1082-1083	2	16
β-strand	1086	1	15
β-strand	1088-1090	3	1
α-helix	1091-1095	5
α-helix	1096-1099	4
α-helix	1102-1109	8
α-helix	1112	1
β-strand	1113-1114	2	17
β-strand	1122-1123	2	17
α-helix	1126-1137	12
α-helix	1143-1145	3

Chain B: 21 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	53-56	4
α-helix	58-60	3
α-helix	64	1
β-strand	65-66	2	18
α-helix	73-74	2
β-strand	78-83	6	18
α-helix	91-92	2
β-strand	96-101	6	18
α-helix	104-114	11
β-strand	119-123	5	18
β-strand	127	1	19
β-strand	132	1	19
β-strand	135-147	13	18
α-helix	149-151	3
β-strand	154-172	19	18
β-strand	178-184	7	18
α-helix	185-187	3
β-strand	188	1	20
α-helix	193-196	4
α-helix	202-206	5
α-helix	209-211	3
α-helix	221-231	11
α-helix	233-237	5
α-helix	242-246	5
α-helix	250-264	15
α-helix	270-272	3
α-helix	277-287	11
α-helix	292-299	8
β-strand	303	1	20
α-helix	304-316	13
β-strand	320-323	4	21
β-strand	330-333	4	21
α-helix	334-336	3
β-strand	337	1	22
β-strand	346-350	5	22
β-strand	356-362	7	22
β-strand	368-375	8	22
β-strand	384-391	8	22
β-strand	397-404	8	22
β-strand	413-418	6	22
α-helix	419-421	3
β-strand	422-424	3	21

Chain C: 13 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	12-13	2	23
β-strand	17-18	2	23
β-strand	21-24	4	24
β-strand	30-35	6	24
β-strand	36	1	23
β-strand	42-49	8	24
α-helix	56-67	12
β-strand	76-78	3	24
β-strand	82	1	24
β-strand	85-91	7	24
β-strand	96	1	25
α-helix	98-104	7
α-helix	112-129	18
β-strand	132-133	2	26
α-helix	139-141	3
β-strand	142	1	27
β-strand	143	1	25
α-helix	147-149	3
β-strand	155	1	27
β-strand	162-163	2	26
α-helix	172-175	4
α-helix	196-198	3
α-helix	200-213	14
α-helix	229-232	4
α-helix	234-240	7
α-helix	245-248	4
α-helix	254-264	11
α-helix	273-286	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA damage-binding protein 1	A	protein	830	Homo sapiens	Q16531 (AlphaFold model)
Protein cereblon	B	protein	382	Homo sapiens	Q96SW2 (AlphaFold model)
Casein kinase I isoform alpha	C	protein	294	Homo sapiens	P48729 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9OTY_1 DNA damage-binding protein 1 (chains A)
MSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGK
IAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGI
IGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICF
VYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYH
NGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDL
RVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIV
DMCVVDLERQGQGQLVTCSGAFKEGSLRIIRLHIRTVPLYESPRKICYQEVSQCFGVLSS
RIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHETSFGEEVEVHNLLIIDQHT
FEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEEAEPKQGRIVVFQYSDGKL
QTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELRTECNHYNNIMALYLKTKG
DFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQ
KDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGETSTPTQGSVLFGTVNGMIG
LVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTERKTEPATGFIDGDLIESFL
DISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIHWSHPQFEK

Sequence of entity 2 (B), FASTA

>9OTY_2 Protein cereblon (chains B)
IINFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFHPQ
EVSMVRNLIQKDRTFAVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIVKVKAIGRQRF
KVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSREDQCSYKWWQ
KYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPIDFSYRVA
ACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGP
MAAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTAT
KKDMSPQKFWGLTRSALLPTIP

Sequence of entity 3 (C), FASTA

>9OTY_3 Casein kinase I isoform alpha (chains C)
EFIVGGKYKLVRKIGSGSFGDIYLAINITNGEEVAVKLESQKARHPQLLYESKLYKILQG
GVGIPHIRWYGQEKDYNVLVMDLLGPSLEDLFNFCSRRFTMKTVLMLADQMISRIEYVHT
KNFIHRDIKPDNFLMGIGRHCNKLFLIDFGLAKKYRDNRTRQHIPYREDKNLTGTARYAS
INAHLGIEQSRRDDMESLGYVLMYFNRTSLPWQGLKAATKKQKYEKISEKKMSTPVEVLC
KGFPAEFAMYLNYCRGLRFEEAPDYMYLRQLFRILFRTLNHQYDYTFDWTMLKQ

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
A1CEH	N-{2-[(3R)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}benzamide	C20 H17 N3 O4	1
A1CEG	N-[3-(benzyloxy)pyridin-2-yl]-N'-(4-cyano-2-hydroxyphenyl)urea	C20 H16 N4 O3	1

Primary citation

Identification of an allosteric site on the E3 ligase adapter cereblon. Dippon, V.N., Rizvi, Z., Choudhry, A.E. et al. Nature (2026) 651:482-490. DOI 10.1038/s41586-025-09994-w · PubMed

Other PDB entries of the same protein (UniProt Q16531 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9BBG 1.7 Å, Co-crystal structure of human DDB1 bound to fragment UB028671
9EJQ 1.87 Å, Crystal structure of DDB1 in complex with XS381952
9BBI 1.9 Å, Co-crystal structure of human DDB1 bound to fragment UB028669
9BZ0 1.9 Å, Structure of an STK19-containing TC-NER complex
9BBE 2.0 Å, Co-crystal structure of human DDB1 bound to fragment UB028668
9BBH 2.0 Å, Co-crystal structure of human DDB1 bound to fragment UB028670
9FJX 2.0 Å, Crystal structure of human CRBN-DDB1 in complex with Lenalidomide
9ZXN 2.07 Å, DDB1 delta with compound 26
37MF 2.1 Å, Crystal structure of DDB1 in complex with XS445479
9ZXM 2.19 Å, DDB1 delta with compound 6
8G46 2.2 Å, Cryo-EM structure of DDB1deltaB-DDA1-DCAF16-BRD4(BD2)-MMH2
8ZSW 2.25 Å, Crystal Structure of Human DDB1, a Component of the E3 Ubiquitin Ligase Complex

Browse structure collections

About this viewer

MolViewer shows 9OTY directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.