5HXB: Cereblon

Name: PDB 5HXB: Cereblon in complex with DDB1, CC-885, and GSPT1
Published: 2016-06-29
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Cereblon in complex with DDB1, CC-885, and GSPT1. Determined by X-ray diffraction at 3.6 Å resolution. Released 29 Jun 2016.

Method: X-ray diffraction
Resolution: 3.6 Å
Organism: Homo sapiens
Chains: 6
Atoms: 25,089
Mol. weight: 392.39 kDa
Ligands: 85C, ZN
Released: 29 Jun 2016

Explore 5HXB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5HXB contains 63 α-helices and 289 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: 0 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	441-443	3	67
β-strand	444-447	4	68
β-strand	450	1	69
β-strand	452	1	69
β-strand	453-457	5	68
β-strand	461	1	67
β-strand	464-465	2	70
β-strand	470-472	3	67
β-strand	477-479	3	67
β-strand	480-486	7	68
β-strand	493-494	2	70
β-strand	500-505	6	68
β-strand	514	1	71
β-strand	516	1	71
β-strand	517-519	3	67
β-strand	528-537	10	72
β-strand	544	1	73
β-strand	548-554	7	72
β-strand	559-566	8	72
β-strand	570	1	74
β-strand	577	1	74
β-strand	585	1	73
β-strand	589	1	72
β-strand	590	1	74
β-strand	592-601	10	72
β-strand	614-619	6	72
β-strand	622-629	8	72
β-strand	633	1	72

Chain B: 15 helices, 101 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	37
β-strand	17-21	5	38
β-strand	30-35	6	38
β-strand	38-43	6	38
β-strand	50-56	7	38
β-strand	61-67	7	39
β-strand	76-81	6	39
β-strand	85-92	8	39
β-strand	99-107	9	39
α-helix	114	1
β-strand	115	1	40
α-helix	116	1
β-strand	121-124	4	41
β-strand	130-134	5	41
β-strand	136	1	40
β-strand	139-144	6	41
β-strand	155-158	4	41
β-strand	164-169	6	42
α-helix	170	1
β-strand	177-184	8	42
β-strand	187-196	10	42
β-strand	201-209	9	42
β-strand	218-221	4	43
β-strand	229-232	4	43
β-strand	237-241	5	43
β-strand	244-248	5	43
α-helix	251-253	3
β-strand	258-263	6	44
β-strand	270-275	6	44
β-strand	279-286	8	44
β-strand	299-307	9	44
α-helix	310	1
β-strand	311-316	6	45
β-strand	321-326	6	45
β-strand	331-336	6	45
β-strand	347-353	7	45
β-strand	359-365	7	46
β-strand	374-379	6	46
α-helix	382-384	3
β-strand	386-393	8	46
β-strand	394	1	47
β-strand	396-403	8	48
β-strand	409-413	5	49
β-strand	422	1	50
β-strand	424-429	6	49
β-strand	432-439	8	49
β-strand	442-446	5	49
β-strand	457-463	7	51
β-strand	467-472	6	51
β-strand	476-480	5	51
β-strand	486-490	5	51
β-strand	500-503	4	52
β-strand	507-512	6	52
β-strand	515-520	6	52
β-strand	522	1	53
β-strand	525	1	53
β-strand	528-531	4	52
β-strand	538-542	5	54
β-strand	555-560	6	54
β-strand	566-570	5	54
β-strand	588-596	9	55
β-strand	599-606	8	55
β-strand	610-615	6	55
β-strand	624	1	55
β-strand	628-630	3	55
β-strand	637-642	6	56
β-strand	647-652	6	56
β-strand	657-660	4	56
β-strand	667-670	4	56
β-strand	671	1	47
β-strand	678-682	5	48
β-strand	684	1	50
β-strand	690-694	5	48
β-strand	698-704	7	48
β-strand	709-716	8	46
β-strand	720-727	8	57
β-strand	732-742	11	57
β-strand	750-751	2	57
α-helix	756-758	3
β-strand	762-764	3	57
β-strand	785-795	11	57
β-strand	801-806	6	57
α-helix	807-808	2
β-strand	811-819	9	58
β-strand	828-835	8	58
β-strand	846-854	9	58
β-strand	857-866	10	58
β-strand	870-876	7	59
β-strand	879-884	6	59
β-strand	887-893	7	59
β-strand	899-906	8	59
β-strand	913-917	5	60
β-strand	920-924	5	60
β-strand	930-936	7	60
β-strand	941-948	8	60
β-strand	954-961	8	61
β-strand	964-969	6	61
β-strand	973-978	6	61
β-strand	991	1	60
β-strand	993-999	7	61
β-strand	1004-1009	6	37
β-strand	1025-1032	8	37
β-strand	1037-1043	7	37
α-helix	1045-1061	17
α-helix	1063-1064	2
α-helix	1070-1074	5
β-strand	1076-1077	2	62
β-strand	1082-1083	2	62
β-strand	1086	1	61
β-strand	1088-1090	3	37
α-helix	1091-1095	5
α-helix	1096-1099	4
α-helix	1102-1108	7
β-strand	1113-1114	2	63
β-strand	1122-1123	2	63
α-helix	1126-1137	12

Chain C: 17 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	54-56	3
α-helix	58-60	3
β-strand	65-66	2	64
α-helix	73-74	2
β-strand	78-83	6	64
β-strand	93	1	64
β-strand	96-101	6	64
α-helix	104-115	12
β-strand	119-124	6	64
β-strand	135-147	13	64
β-strand	154-172	19	64
β-strand	178-184	7	64
α-helix	185-187	3
α-helix	200-205	6
α-helix	209-211	3
α-helix	222-231	10
α-helix	233-237	5
α-helix	242-245	4
α-helix	246-248	3
α-helix	250-262	13
α-helix	277-287	11
α-helix	292-300	9
α-helix	304-317	14
β-strand	320-323	4	65
β-strand	330-333	4	65
α-helix	334-336	3
β-strand	337	1	66
β-strand	346-350	5	66
β-strand	356-362	7	66
β-strand	368-375	8	66
β-strand	384-391	8	66
β-strand	397-404	8	66
β-strand	413-418	6	66
α-helix	419-421	3
β-strand	422-425	4	65

Chain X: 0 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	441-443	3	1
β-strand	444-447	4	2
β-strand	455-457	3	2
β-strand	461	1	1
β-strand	464-465	2	3
β-strand	470-472	3	1
β-strand	477-479	3	1
β-strand	480-484	5	2
β-strand	493-494	2	3
β-strand	501-505	5	2
β-strand	517-519	3	1
β-strand	528-536	9	4
β-strand	537	1	5
β-strand	548-554	7	4
β-strand	557-566	10	4
β-strand	570	1	6
β-strand	577	1	6
β-strand	589	1	5
β-strand	590	1	6
β-strand	592-601	10	4
β-strand	614-619	6	4
β-strand	622-629	8	4
β-strand	633	1	4

Chain Y: 13 helices, 101 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	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	85-92	8	9
β-strand	99-107	9	9
α-helix	114	1
β-strand	115	1	10
α-helix	116	1
β-strand	121-124	4	11
β-strand	130-134	5	11
β-strand	136	1	10
β-strand	139-144	6	11
β-strand	155-158	4	11
β-strand	164-169	6	12
α-helix	170	1
β-strand	177-184	8	12
β-strand	187-196	10	12
β-strand	201-208	8	12
β-strand	218-221	4	13
β-strand	229-232	4	13
β-strand	237-241	5	13
β-strand	244-248	5	13
α-helix	251-253	3
β-strand	258-263	6	14
β-strand	270-275	6	14
β-strand	279-286	8	14
β-strand	299-307	9	14
α-helix	310	1
β-strand	311-316	6	15
β-strand	321-326	6	15
β-strand	331-336	6	15
β-strand	347-353	7	15
β-strand	359-365	7	16
β-strand	374-379	6	16
α-helix	382-384	3
β-strand	386-393	8	16
β-strand	394	1	17
β-strand	396-403	8	18
β-strand	409-413	5	19
β-strand	422	1	20
β-strand	424-429	6	19
β-strand	432-439	8	19
β-strand	442-446	5	19
β-strand	457-463	7	21
β-strand	467-472	6	21
β-strand	476-480	5	21
β-strand	486-490	5	21
β-strand	500-503	4	22
β-strand	507-512	6	22
β-strand	515-520	6	22
β-strand	522	1	23
β-strand	525	1	23
β-strand	528-531	4	22
β-strand	538-542	5	24
β-strand	555-560	6	24
β-strand	566-570	5	24
β-strand	580	1	24
β-strand	588-596	9	25
β-strand	599-606	8	25
β-strand	610-616	7	25
β-strand	623-630	8	25
β-strand	637-642	6	26
β-strand	647-652	6	26
β-strand	657-660	4	26
β-strand	667-670	4	26
β-strand	671	1	17
β-strand	678-682	5	18
β-strand	684	1	20
β-strand	690-694	5	18
β-strand	698-704	7	18
β-strand	709-716	8	16
β-strand	720-727	8	27
β-strand	732-742	11	27
β-strand	750-751	2	27
α-helix	756-758	3
β-strand	762-765	4	27
β-strand	785-795	11	27
β-strand	801-806	6	27
β-strand	811-819	9	28
β-strand	828-835	8	28
β-strand	846-854	9	28
β-strand	857-866	10	28
β-strand	870-876	7	29
β-strand	879-884	6	29
β-strand	887-893	7	29
β-strand	899-906	8	29
β-strand	913-917	5	30
β-strand	920-924	5	30
β-strand	930-936	7	30
β-strand	941-948	8	30
β-strand	954-961	8	31
β-strand	964-969	6	31
β-strand	973-978	6	31
β-strand	991	1	30
β-strand	993-999	7	31
β-strand	1004-1009	6	7
β-strand	1025-1032	8	7
β-strand	1037-1043	7	7
α-helix	1045-1061	17
α-helix	1070-1074	5
β-strand	1076-1077	2	32
β-strand	1082-1083	2	32
β-strand	1086	1	31
β-strand	1088-1090	3	7
α-helix	1091-1095	5
α-helix	1096-1099	4
α-helix	1102-1108	7
β-strand	1113-1114	2	33
β-strand	1122-1123	2	33
α-helix	1126-1137	12

Chain Z: 18 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	54-56	3
α-helix	58-60	3
β-strand	65-66	2	34
α-helix	73-74	2
β-strand	78-83	6	34
β-strand	93	1	34
β-strand	96-101	6	34
α-helix	104-115	12
β-strand	119-124	6	34
α-helix	127-129	3
β-strand	135-147	13	34
β-strand	154-171	18	34
β-strand	178-184	7	34
α-helix	185-187	3
α-helix	200-205	6
α-helix	209-212	4
α-helix	222-231	10
α-helix	233-237	5
α-helix	242-245	4
α-helix	246-248	3
α-helix	250-263	14
α-helix	277-287	11
α-helix	292-300	9
α-helix	304-317	14
β-strand	320-323	4	35
β-strand	330-333	4	35
α-helix	334-336	3
β-strand	337	1	36
β-strand	346-350	5	36
β-strand	356-362	7	36
β-strand	368-375	8	36
β-strand	384-391	8	36
β-strand	397-404	8	36
β-strand	413-418	6	36
α-helix	419-421	3
β-strand	422-425	4	35

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

>5HXB_1 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A (chains A, X)
GSGPIRLPIVDKYKDMGTVVLGKLESGSICKGQQLVMMPNKHNVEVLGILSDDVETDTVA
PGENLKIRLKGIEEEEILPGFILCDPNNLCHSGRTFDAQIVIIEHKSIICPGYNAVLHIH
TCIEEVEITALICLVDKKSGEKSKTRPRFVKQDQVCIARLRTAGTICLETFKDFPQMGRF
TLRDEGKTIAIGKVLKLVP

Sequence of entity 2 (B, Y), FASTA

>5HXB_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

>5HXB_3 Protein cereblon (chains C, Z)
GSMEAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQT
LPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIVK
VKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSRE
DQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSN
PIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNE
IFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICAS
HIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPDKVILCL

Ligands and cofactors

ID	Name	Formula	Copies
85C	1-(3-chloro-4-methylphenyl)-3-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihy…	C22 H21 Cl N4 O4	2
ZN	Zinc ion	Zn	2

Primary citation

A novel cereblon modulator recruits GSPT1 to the CRL4(CRBN) ubiquitin ligase. Matyskiela, M.E., Lu, G., Ito, T. et al. Nature (2016) 535:252-257. DOI 10.1038/nature18611 · 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
6XK9 3.64 Å, Cereblon in complex with DDB1, CC-90009, 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…

Browse structure collections

About this viewer

MolViewer shows 5HXB 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.