6XK9: Cereblon

Name: PDB 6XK9: Cereblon in complex with DDB1, CC-90009, and GSPT1
Published: 2020-12-02
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Cereblon in complex with DDB1, CC-90009, and GSPT1. Determined by X-ray diffraction at 3.64 Å resolution. Released 2 Dec 2020.

Method: X-ray diffraction
Resolution: 3.64 Å
Organism: Homo sapiens
Chains: 6
Atoms: 25,483
Mol. weight: 392.43 kDa
Ligands: ZN, V4M
Released: 2 Dec 2020

Explore 6XK9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6XK9 contains 74 α-helices and 305 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: 1 helix, 23 β-strands

Element	Residues	Length	Sheet
β-strand	440-442	3	41
β-strand	443-447	5	42
β-strand	453-457	5	42
β-strand	460	1	41
β-strand	463	1	43
β-strand	469-471	3	41
β-strand	476-478	3	41
β-strand	480-483	4	42
β-strand	493	1	43
β-strand	498-503	6	42
β-strand	513	1	44
β-strand	515	1	44
β-strand	516-518	3	41
β-strand	529-536	8	45
β-strand	543	1	46
β-strand	548-553	6	45
β-strand	556-569	14	45
β-strand	576	1	45
α-helix	580-581	2
β-strand	584	1	46
β-strand	588-596	9	45
β-strand	613-618	6	45
β-strand	621-628	8	45
β-strand	632	1	45

Chain B: 17 helices, 109 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	47
β-strand	17-21	5	48
β-strand	30-35	6	48
β-strand	38-43	6	48
β-strand	50-56	7	48
β-strand	61-67	7	49
β-strand	76-81	6	49
β-strand	85-92	8	49
β-strand	99-107	9	49
β-strand	115	1	50
β-strand	121-124	4	51
β-strand	130-134	5	51
β-strand	136	1	50
β-strand	139	1	52
β-strand	141-144	4	51
β-strand	155	1	51
β-strand	158	1	52
β-strand	164-169	6	53
α-helix	170	1
β-strand	177-184	8	53
β-strand	187-195	9	53
β-strand	202-208	7	53
β-strand	218-221	4	54
β-strand	229-232	4	54
β-strand	237-240	4	54
β-strand	241	1	55
β-strand	244	1	55
β-strand	247-248	2	54
β-strand	258-263	6	56
β-strand	270-275	6	56
β-strand	279-285	7	56
β-strand	300-307	8	56
β-strand	311-316	6	57
β-strand	321-326	6	57
β-strand	331-335	5	57
α-helix	340-341	2
β-strand	348-353	6	57
β-strand	359-365	7	58
β-strand	372	1	59
β-strand	374-379	6	58
α-helix	382-384	3
β-strand	386-393	8	58
β-strand	394	1	60
β-strand	396-403	8	61
β-strand	410-413	4	62
β-strand	424-429	6	62
β-strand	432-439	8	62
β-strand	442-446	5	62
β-strand	459-460	2	63
β-strand	463	1	63
β-strand	467-471	5	63
β-strand	476-480	5	63
β-strand	486-488	3	63
α-helix	496-498	3
β-strand	500-503	4	64
β-strand	507-512	6	64
β-strand	515-522	8	64
β-strand	525-528	4	64
β-strand	533	1	64
β-strand	538-542	5	65
β-strand	555-560	6	65
β-strand	565-570	6	65
β-strand	575-581	7	65
α-helix	582-583	2
α-helix	587	1
β-strand	588-596	9	66
β-strand	599-606	8	66
β-strand	610-616	7	66
β-strand	623-630	8	66
β-strand	637-643	7	67
β-strand	646-652	7	67
β-strand	653	1	68
β-strand	657-662	6	67
β-strand	665-670	6	67
β-strand	671	1	60
β-strand	676	1	68
β-strand	678-682	5	61
β-strand	690-694	5	61
β-strand	698-704	7	61
β-strand	709-716	8	58
β-strand	720-727	8	69
α-helix	728-730	3
β-strand	732-742	11	69
β-strand	750-751	2	69
β-strand	762-763	2	69
β-strand	785-795	11	69
β-strand	801-806	6	69
β-strand	811-813	3	70
β-strand	817-819	3	71
β-strand	828-832	5	71
β-strand	833-835	3	70
β-strand	846-854	9	71
β-strand	857-866	10	71
β-strand	873-876	4	72
β-strand	879-884	6	72
β-strand	887-893	7	72
β-strand	899-906	8	72
β-strand	913-915	3	73
β-strand	920-924	5	73
β-strand	930-936	7	73
β-strand	941-948	8	73
β-strand	954-959	6	74
β-strand	964-969	6	74
β-strand	973-978	6	74
β-strand	991	1	73
α-helix	992	1
β-strand	993-999	7	74
β-strand	1004-1009	6	47
β-strand	1014	1	59
β-strand	1025-1032	8	47
β-strand	1037-1042	6	47
α-helix	1045-1061	17
α-helix	1063-1064	2
α-helix	1065-1067	3
α-helix	1070-1074	5
β-strand	1076-1077	2	75
β-strand	1082-1083	2	75
β-strand	1086	1	74
β-strand	1090	1	47
α-helix	1091-1095	5
α-helix	1096-1098	3
α-helix	1102-1108	7
β-strand	1113-1114	2	76
β-strand	1122-1123	2	76
α-helix	1126-1136	11
α-helix	1137-1139	3

Chain C: 19 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	53-56	4
α-helix	58-60	3
α-helix	63-64	2
β-strand	65-66	2	77
α-helix	73-74	2
β-strand	78-83	6	77
α-helix	91-92	2
β-strand	96-101	6	77
α-helix	104-115	12
β-strand	119-124	6	77
β-strand	135-147	13	77
β-strand	154-172	19	77
β-strand	178-184	7	77
α-helix	185-186	2
β-strand	188	1	78
α-helix	195-197	3
α-helix	200-205	6
α-helix	209-212	4
α-helix	221-231	11
α-helix	233-237	5
α-helix	242-246	5
α-helix	250-261	12
α-helix	277-286	10
α-helix	292-300	9
β-strand	303	1	78
α-helix	304-317	14
β-strand	320-323	4	79
β-strand	330-333	4	79
α-helix	334-336	3
β-strand	337	1	80
β-strand	341	1	81
β-strand	344	1	81
β-strand	346-350	5	80
β-strand	356-362	7	80
β-strand	368-370	3	80
β-strand	375	1	80
β-strand	384-391	8	80
β-strand	397-404	8	80
β-strand	413-418	6	80
α-helix	419-421	3
β-strand	422-425	4	79

Chain X: 1 helix, 22 β-strands

Element	Residues	Length	Sheet
β-strand	440-442	3	1
β-strand	443-447	5	2
β-strand	453-457	5	2
β-strand	460	1	1
β-strand	463	1	3
β-strand	469-471	3	1
β-strand	476-478	3	1
β-strand	479-483	5	2
β-strand	493	1	3
β-strand	498-504	7	2
β-strand	513	1	4
β-strand	515	1	4
β-strand	516-518	3	1
β-strand	527-536	10	5
β-strand	543	1	6
β-strand	548-553	6	5
β-strand	556-569	14	5
β-strand	576	1	5
α-helix	580-581	2
β-strand	584	1	6
β-strand	588-600	13	5
β-strand	613-618	6	5
β-strand	621-628	8	5

Chain Y: 16 helices, 107 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	7
β-strand	17-21	5	8
β-strand	30-35	6	8
β-strand	38-43	6	8
β-strand	50-56	7	8
β-strand	61-67	7	9
β-strand	76-81	6	9
β-strand	85-93	9	9
β-strand	98-107	10	9
β-strand	115	1	10
β-strand	121-124	4	11
β-strand	130-134	5	11
β-strand	136	1	10
β-strand	139	1	12
β-strand	141-144	4	11
β-strand	155	1	11
β-strand	158	1	12
β-strand	164-169	6	13
α-helix	170	1
β-strand	177-184	8	13
β-strand	187-195	9	13
β-strand	202-204	3	13
β-strand	218-221	4	14
β-strand	229-232	4	14
β-strand	237-240	4	14
β-strand	241	1	15
β-strand	244	1	15
β-strand	247-248	2	14
α-helix	251-253	3
β-strand	258-263	6	16
β-strand	270-275	6	16
β-strand	279-288	10	16
β-strand	296-307	12	16
β-strand	311-316	6	17
β-strand	321-326	6	17
β-strand	331-336	6	17
α-helix	340-341	2
β-strand	347-353	7	17
β-strand	359-365	7	18
β-strand	374-379	6	18
α-helix	382-384	3
β-strand	386-393	8	18
β-strand	394	1	19
β-strand	396-403	8	20
β-strand	409-413	5	21
β-strand	424-429	6	21
β-strand	432-439	8	21
β-strand	442-445	4	21
β-strand	459-460	2	22
β-strand	463	1	22
β-strand	467-471	5	22
β-strand	475-480	6	22
β-strand	486-491	6	22
α-helix	496-498	3
β-strand	500-503	4	23
β-strand	507-512	6	23
β-strand	515-522	8	23
β-strand	525-528	4	23
β-strand	533	1	23
β-strand	538-542	5	24
β-strand	555-560	6	24
β-strand	565-570	6	24
β-strand	575-581	7	24
β-strand	588-596	9	25
β-strand	599-606	8	25
β-strand	610-617	8	25
β-strand	622-630	9	25
β-strand	637-643	7	26
β-strand	646-652	7	26
β-strand	653	1	27
β-strand	657-660	4	26
β-strand	667-670	4	26
β-strand	671	1	19
β-strand	676	1	27
β-strand	678-682	5	20
β-strand	690-694	5	20
β-strand	698-704	7	20
β-strand	709-716	8	18
β-strand	720-727	8	28
α-helix	728-730	3
β-strand	732-742	11	28
β-strand	750-751	2	28
β-strand	762-763	2	28
β-strand	785-795	11	28
β-strand	801-806	6	28
β-strand	811-813	3	29
β-strand	817-819	3	30
β-strand	828-832	5	30
β-strand	833-835	3	29
β-strand	846-854	9	30
β-strand	857-866	10	30
β-strand	873-876	4	31
β-strand	879-884	6	31
β-strand	887-893	7	31
β-strand	899-906	8	31
β-strand	913-915	3	32
β-strand	920-924	5	32
β-strand	930-936	7	32
β-strand	941-948	8	32
β-strand	954-959	6	33
β-strand	964-969	6	33
β-strand	973-978	6	33
β-strand	991	1	32
α-helix	992	1
β-strand	993-999	7	33
β-strand	1004-1009	6	7
β-strand	1025-1032	8	7
β-strand	1037-1042	6	7
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	34
β-strand	1082-1083	2	34
β-strand	1086	1	33
β-strand	1090	1	7
α-helix	1091-1095	5
α-helix	1096-1098	3
α-helix	1102-1108	7
β-strand	1113-1114	2	35
β-strand	1122-1123	2	35
α-helix	1126-1136	11
α-helix	1137-1139	3

Chain Z: 20 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	53-56	4
α-helix	58-60	3
α-helix	63-64	2
β-strand	65-66	2	36
α-helix	73-74	2
β-strand	78-83	6	36
α-helix	91-92	2
β-strand	96-101	6	36
α-helix	104-115	12
β-strand	119-124	6	36
β-strand	135-147	13	36
β-strand	154-172	19	36
β-strand	178-184	7	36
α-helix	185-186	2
β-strand	188	1	37
α-helix	195-197	3
α-helix	200-205	6
α-helix	209-212	4
α-helix	221-231	11
α-helix	233-237	5
α-helix	242-246	5
α-helix	250-262	13
α-helix	269-272	4
α-helix	277-286	10
α-helix	292-300	9
β-strand	303	1	37
α-helix	304-317	14
β-strand	320-323	4	38
β-strand	330-333	4	38
α-helix	334-336	3
β-strand	337	1	39
β-strand	341	1	40
β-strand	344	1	40
β-strand	346-350	5	39
β-strand	356-362	7	39
β-strand	368-370	3	39
β-strand	375	1	39
β-strand	384-391	8	39
β-strand	397-404	8	39
β-strand	413-418	6	39
α-helix	419-421	3
β-strand	422-425	4	38

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Eukaryotic peptide chain release factor GTP-binding subunit ERF3A	A, X	protein	199	Homo sapiens	P15170 (AlphaFold model)
DNA damage-binding protein 1	B, Y	protein	1140	Homo sapiens	Q16531 (AlphaFold model)
Protein cereblon	C, Z	protein	406	Homo sapiens	Q96SW2 (AlphaFold model)

Sequence of entity 1 (A, X), FASTA

>6XK9_1 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A (chains A, X)
GSGPIRLPIVDKYKDMGTVVLGKLESGSICKGQQLVMMPNKHNVEVLGILSDDVETDTVA
PGENLKIRLKGIEEEEILPGFILCDPNNLCHSGRTFDAQIVIIEHKSIICPGYNAVLHIH
TCIEEVEITALICLVDKKSGEKSKTRPRFVKQDQVCIARLRTAGTICLETFKDFPQMGRF
TLRDEGKTIAIGKVLKLVP

Sequence of entity 2 (B, Y), FASTA

>6XK9_2 DNA damage-binding protein 1 (chains B, Y)
MSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGK
IAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGI
IGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICF
VYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYH
NGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDL
RVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIV
DMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGIHEHASIDLPGIKGLWPLRSDPNRE
TDDTLVLSFVGQTRVLMLNGEEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVS
QEPKALVSEWKEPQAKNISVASCNSSQVVVAVGRALYYLQIHPQELRQISHTEMEHEVAC
LDITPLGDSNGLSPLCAIGLWTDISARILKLPSFELLHKEMLGGEIIPRSILMTTFESSH
YLLCALGDGALFYFGLNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTVIY
SSNHKLVFSNVNLKEVNYMCPLNSDGYPDSLALANNSTLTIGTIDEIQKLHIRTVPLYES
PRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHET
SFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEE
AEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELR
TECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEIL
DDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGET
STPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTER
KTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH

Sequence of entity 3 (C, Z), FASTA

>6XK9_3 Protein cereblon (chains C, Z)
GSMEAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQT
LPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIVK
VKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSRE
DQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSN
PIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNE
IFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICAS
HIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPDKVILCL

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
V4M	2-(4-chlorophenyl)-N-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-is…	C22 H18 Cl F2 N3 O4	2

Primary citation

CC-90009, a novel cereblon E3 ligase modulator, targets acute myeloid leukemia blasts and leukemia stem cells. Surka, C., Jin, L., Mbong, N. et al. Blood (2021) 137:661-677. DOI 10.1182/blood.2020008676 · PubMed

Other PDB entries of the same protein (UniProt P15170 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3KUI 2.3 Å, Crystal structure of C-terminal domain of PABPC1 in complex with binding region of eRF3a
12BP 2.9 Å, Cryo-EM structure of human DDB1-CRBN-GSPT1 in complex with GT19630
5HXB 3.6 Å, Cereblon in complex with DDB1, CC-885, and GSPT1
5LZT 3.65 Å, Structure of the mammalian ribosomal termination complex with eRF1 and eRF3.
3E1Y 3.8 Å, Crystal structure of human eRF1/eRF3 complex
9HNE 3.9 Å, Cereblon in complex with DDB1, GSPT1 and Compound-1
4D61 9.0 Å, Cryo-EM structures of ribosomal 80S complexes with termination factors and cricket…
3J5Y 9.7 Å, Structure of the mammalian ribosomal pre-termination complex associated with…

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