8G66: Structure with SJ3149

Name: PDB 8G66: Structure with SJ3149
Published: 2023-12-13
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Structure with SJ3149. Determined by X-ray diffraction at 3.45 Å resolution. Released 13 Dec 2023.

Method: X-ray diffraction
Resolution: 3.45 Å
Organism: Homo sapiens
Chains: 6
Atoms: 21,297
Mol. weight: 369.13 kDa
Ligands: YOT, ZN
Released: 13 Dec 2023

Explore 8G66 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8G66 contains 91 α-helices and 210 β-strands across 6 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: 13 helices, 72 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	1
β-strand	17-21	5	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	122-124	3	5
β-strand	130-133	4	5
β-strand	136	1	4
β-strand	139-144	6	5
β-strand	155-158	4	5
β-strand	164-169	6	6
β-strand	177-183	7	6
β-strand	188-196	9	6
β-strand	201-204	4	6
β-strand	210-212	3	6
β-strand	218-221	4	7
β-strand	229-232	4	7
β-strand	237-241	5	7
β-strand	244-245	2	7
β-strand	248	1	7
α-helix	251-253	3
β-strand	258-263	6	8
β-strand	271-275	5	8
β-strand	279-283	5	8
β-strand	302-307	6	8
α-helix	310-311	2
β-strand	313-316	4	9
β-strand	321-325	5	9
β-strand	331-336	6	9
β-strand	347-353	7	9
β-strand	359-365	7	10
β-strand	372	1	11
β-strand	374-379	6	10
α-helix	382-384	3
β-strand	386-391	6	10
β-strand	711-716	6	10
β-strand	720-727	8	12
α-helix	728-730	3
β-strand	732-743	12	12
β-strand	749-751	3	12
β-strand	762-765	4	12
β-strand	785-795	11	12
β-strand	801-806	6	12
β-strand	811-820	10	13
β-strand	827-835	9	13
β-strand	846-854	9	13
β-strand	857-866	10	13
β-strand	870-876	7	14
β-strand	879-884	6	14
β-strand	887-893	7	14
β-strand	899-903	5	14
β-strand	906	1	14
β-strand	914-917	4	15
β-strand	920-923	4	15
β-strand	930-934	5	15
β-strand	935-936	2	16
β-strand	941-942	2	16
β-strand	946-948	3	15
β-strand	954-959	6	17
β-strand	964-969	6	17
β-strand	973-978	6	17
α-helix	986-989	4
β-strand	991	1	15
β-strand	993-999	7	17
β-strand	1004-1009	6	1
β-strand	1014	1	11
β-strand	1025-1032	8	1
β-strand	1037-1042	6	1
α-helix	1045-1061	17
α-helix	1070-1074	5
β-strand	1076-1077	2	18
β-strand	1082-1083	2	18
β-strand	1086	1	17
β-strand	1088-1090	3	1
α-helix	1091-1094	4
α-helix	1095-1099	5
α-helix	1102-1108	7
α-helix	1126-1137	12

Chain B: 19 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	52-56	5
α-helix	58-60	3
α-helix	63-64	2
β-strand	65-66	2	19
α-helix	73-74	2
β-strand	78-83	6	19
β-strand	96-101	6	19
α-helix	104-115	12
β-strand	119-127	9	19
β-strand	132-149	18	19
β-strand	152-172	21	19
β-strand	178-184	7	19
α-helix	185-186	2
β-strand	188	1	20
α-helix	195-197	3
α-helix	201-205	5
α-helix	221-231	11
α-helix	233-236	4
α-helix	242-245	4
α-helix	246-248	3
α-helix	250-264	15
α-helix	269-272	4
α-helix	277-286	10
α-helix	292-300	9
β-strand	303	1	20
α-helix	304-317	14
β-strand	320-323	4	21
β-strand	330-333	4	21
α-helix	334-336	3
β-strand	337	1	22
β-strand	341	1	23
β-strand	344	1	23
β-strand	346-350	5	22
β-strand	356-362	7	22
β-strand	368-370	3	22
β-strand	375	1	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	422-425	4	21

Chain C: 19 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	12-13	2	24
β-strand	17-22	6	24
β-strand	31-36	6	24
β-strand	42-49	8	24
α-helix	57-66	10
α-helix	74-75	2
β-strand	76-82	7	24
β-strand	85-90	6	24
β-strand	96	1	25
α-helix	97-103	7
α-helix	110-129	20
β-strand	132-133	2	26
α-helix	139-141	3
β-strand	142-144	3	25
α-helix	147-149	3
β-strand	153-155	3	25
α-helix	158-160	3
β-strand	162-163	2	26
β-strand	165	1	27
α-helix	171	1
β-strand	172	1	27
α-helix	173-175	3
α-helix	185-187	3
α-helix	190-193	4
α-helix	196-198	3
α-helix	200-215	16
α-helix	229-242	14
α-helix	245-248	4
α-helix	254-265	12
α-helix	270-272	3
α-helix	274-287	14
α-helix	297-301	5

Chain D: 14 helices, 68 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	28
β-strand	17-21	5	29
β-strand	30-35	6	29
β-strand	38-44	7	29
β-strand	49-56	8	29
β-strand	61-67	7	30
β-strand	76-81	6	30
β-strand	85-94	10	30
β-strand	97-107	11	30
β-strand	115	1	31
β-strand	121-124	4	32
β-strand	130-134	5	32
β-strand	136	1	31
β-strand	139-144	6	32
β-strand	155-158	4	32
β-strand	164-169	6	33
α-helix	170	1
β-strand	177-183	7	33
β-strand	188-196	9	33
β-strand	201-204	4	33
β-strand	210-211	2	33
β-strand	218-221	4	34
β-strand	229-232	4	34
β-strand	237-241	5	34
β-strand	244-248	5	34
α-helix	251-253	3
β-strand	258-263	6	35
β-strand	270-275	6	35
β-strand	279-289	11	35
β-strand	295-307	13	35
α-helix	310-311	2
β-strand	313-318	6	36
β-strand	321-325	5	36
β-strand	331-336	6	36
β-strand	347-353	7	36
β-strand	359-365	7	37
β-strand	372	1	38
β-strand	374-379	6	37
α-helix	382-384	3
β-strand	386-391	6	37
β-strand	711-716	6	37
β-strand	720-727	8	39
α-helix	728-730	3
β-strand	732-743	12	39
β-strand	749-751	3	39
β-strand	762-765	4	39
α-helix	766-768	3
β-strand	785-795	11	39
β-strand	801-806	6	39
β-strand	811-820	10	40
β-strand	827-835	9	40
β-strand	846-854	9	40
β-strand	857-866	10	40
β-strand	870-875	6	41
β-strand	880-884	5	41
β-strand	887-893	7	41
β-strand	899-906	8	41
β-strand	913-917	5	42
β-strand	920-924	5	42
β-strand	930-936	7	42
β-strand	941-948	8	42
β-strand	954-961	8	43
β-strand	964-969	6	43
β-strand	973-978	6	43
β-strand	991	1	42
β-strand	993-999	7	43
β-strand	1004-1009	6	28
β-strand	1014	1	38
β-strand	1025-1032	8	28
β-strand	1037-1042	6	28
α-helix	1045-1061	17
α-helix	1063-1064	2
α-helix	1065-1067	3
α-helix	1070-1073	4
β-strand	1076-1077	2	44
β-strand	1082-1083	2	44
β-strand	1086	1	43
β-strand	1088-1090	3	28
α-helix	1091-1095	5
α-helix	1096-1099	4
α-helix	1102-1109	8
α-helix	1126-1139	14

Chain E: 10 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	78-80	3	45
β-strand	83	1	45
β-strand	93	1	45
β-strand	96-99	4	45
α-helix	111-115	5
β-strand	120-123	4	45
β-strand	135-141	7	45
β-strand	157-166	10	45
β-strand	181-184	4	45
β-strand	188	1	46
α-helix	220-231	12
α-helix	233-237	5
α-helix	242-246	5
α-helix	250-264	15
α-helix	277-286	10
α-helix	292-300	9
β-strand	303	1	46
α-helix	304-317	14
β-strand	320-323	4	47
β-strand	330-333	4	47
α-helix	334-336	3
β-strand	337	1	48
β-strand	346-350	5	48
β-strand	356-362	7	48
β-strand	368-375	8	48
β-strand	384-391	8	48
β-strand	397-404	8	48
β-strand	413-418	6	48
α-helix	419-421	3
β-strand	422-425	4	47

Chain F: 16 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	12-13	2	49
β-strand	17-25	9	49
β-strand	30-36	7	49
β-strand	42-49	8	49
α-helix	57-67	11
β-strand	68	1	50
β-strand	70	1	50
β-strand	76-82	7	49
β-strand	85-90	6	49
β-strand	96	1	51
α-helix	97-103	7
α-helix	110-129	20
β-strand	132-133	2	52
β-strand	142-144	3	51
α-helix	147-149	3
β-strand	153-155	3	51
α-helix	158-160	3
β-strand	162-163	2	52
β-strand	165	1	53
α-helix	171	1
β-strand	172	1	53
α-helix	173-175	3
α-helix	190-193	4
α-helix	196-198	3
α-helix	200-215	16
α-helix	229-242	14
α-helix	245-248	4
α-helix	254-264	11
α-helix	270-272	3
α-helix	274-287	14
α-helix	297-302	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA damage-binding protein 1	A, D	protein	860	Homo sapiens	Q16531 (AlphaFold model)
Protein cereblon	B, E	protein	426	Homo sapiens	Q96SW2 (AlphaFold model)
Casein kinase I isoform alpha	C, F	protein	341	Homo sapiens	P48729 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>8G66_1 DNA damage-binding protein 1 (chains A, D)
MGSSHHHHHHSAVDENLYFQGGGRMSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKN
TRLEIYVVTAEGLRPVKEVGMYGKIAVMELFRPKGESKDLLFILTAKYNACILEYKQSGE
SIDIITRAHGNVQDRIGRPSETGIIGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFN
IRLEELHVIDVKFLYGCQAPTICFVYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEA
SMVIAVPEPFGGAIIIGQESITYHNGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDM
EGRLFMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKL
NVDSNEQGSYVVAMETFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGG
NGNSGEIQKLHIRTVPLYESPRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQA
LSSSVSSSKLFSSSTAPHETSFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCK
LGKDPNTYFIVGTAMVYPEEAEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKL
LASINSTVRLYEWTTEKELRTECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEG
NFEEIARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHL
GEFVNVFCHGSLVMQNLGETSTPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNK
VIKSVGKIEHSFWRSFHTERKTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGM
KREATADDLIKVVEELTRIH

Sequence of entity 2 (B, E), FASTA

>8G66_2 Protein cereblon (chains B, E)
MDWSHPQFEKSAVDENLYFQGGGRAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDD
SCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFG
TTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSA
VQLESLNKCQIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDR
IKKQLREWDENLKDDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMN
KCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPST
EHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPD
KVILCL

Sequence of entity 3 (C, F), FASTA

>8G66_3 Casein kinase I isoform alpha (chains C, F)
GGGRMASSSGSKAEFIVGGKYKLVRKIGSGSFGDIYLAINITNGEEVAVKLESQKARHPQ
LLYESKLYKILQGGVGIPHIRWYGQEKDYNVLVMDLLGPSLEDLFNFCSRRFTMKTVLML
ADQMISRIEYVHTKNFIHRDIKPDNFLMGIGRHCNKLFLIDFGLAKKYRDNRTRQHIPYR
EDKNLTGTARYASINAHLGIEQSRRDDMESLGYVLMYFNRTSLPWQGLKAATKKQKYEKI
SEKKMSTPVEVLCKGFPAEFAMYLNYCRGLRFEEAPDYMYLRQLFRILFRTLNHQYDYTF
DWTMLKQKAAQQAASSSGQGQQAQTPTGKQTDKTKSNMKGF

Ligands and cofactors

ID	Name	Formula	Copies
YOT	(3S)-3-{5-[(1,2-benzoxazol-3-yl)amino]-1-oxo-1,3-dihydro-2H-isoindol-2-yl}piper…	C20 H16 N4 O4	1
ZN	Zinc ion	Zn	2

Primary citation

Structure of ternary complex with molecular glue targeting CK1A for degradation by the CRL4CRBN ubiquitin ligase. Miller, D.J., Young, S.M., Fischer, M. To be published.

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

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