5FQD: DNA damage-binding protein 1

Name: PDB 5FQD: Structural basis of Lenalidomide induced CK1a degradation by the crl4crbn ubiquitin ligase
Published: 2016-02-24
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Structural basis of Lenalidomide induced CK1a degradation by the crl4crbn ubiquitin ligase. Determined by X-ray diffraction at 2.45 Å resolution. Released 24 Feb 2016.

Method: X-ray diffraction
Resolution: 2.45 Å
Organism: HOMO SAPIENS
Chains: 6
Atoms: 23,544
Mol. weight: 368.75 kDa
Ligands: ZN, LVY
Released: 24 Feb 2016

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

Secondary structure: helices and β-sheets

5FQD contains 91 α-helices and 200 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: 12 helices, 66 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
β-strand	115	1	4
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	177-184	8	6
β-strand	187-196	10	6
β-strand	201-204	4	6
β-strand	210-211	2	6
β-strand	218-221	4	7
β-strand	229-232	4	7
β-strand	237-240	4	7
β-strand	245-248	4	7
α-helix	251-253	3
β-strand	258-263	6	8
β-strand	270-275	6	8
β-strand	279-286	8	8
β-strand	299-307	9	8
β-strand	311-318	8	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	386-392	7	10
β-strand	710-716	7	10
β-strand	720-727	8	11
β-strand	732-743	12	11
α-helix	744	1
β-strand	749-751	3	11
β-strand	762-765	4	11
α-helix	766-768	3
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	899-906	8	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	954-959	6	15
β-strand	964-969	6	15
β-strand	973-978	6	15
α-helix	988-990	3
β-strand	991	1	14
β-strand	993-999	7	15
β-strand	1004-1009	6	1
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	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	1102-1108	7
α-helix	1126-1137	12

Chain B: 19 helices, 21 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	17
α-helix	73-74	2
β-strand	78-83	6	17
α-helix	91-92	2
β-strand	96-101	6	17
α-helix	104-115	12
β-strand	119-127	9	17
β-strand	132-149	18	17
β-strand	152-172	21	17
β-strand	178-184	7	17
α-helix	185-186	2
β-strand	188	1	18
α-helix	195-197	3
α-helix	200-205	6
α-helix	220-231	12
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	292-299	8
β-strand	303	1	18
α-helix	304-317	14
β-strand	320-323	4	19
β-strand	330-333	4	19
α-helix	334-336	3
β-strand	337	1	20
β-strand	341	1	21
β-strand	344	1	21
β-strand	346-350	5	20
β-strand	356-362	7	20
β-strand	368-375	8	20
β-strand	384-391	8	20
β-strand	397-404	8	20
β-strand	413-418	6	20
α-helix	419-421	3
β-strand	422-425	4	19

Chain C: 17 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	12-13	2	22
β-strand	17-24	8	22
β-strand	29-36	8	22
β-strand	42-49	8	22
α-helix	57-67	11
α-helix	74-75	2
β-strand	76-82	7	22
β-strand	85-91	7	22
β-strand	96	1	23
α-helix	97-103	7
α-helix	110-129	20
β-strand	132-133	2	24
α-helix	139-141	3
β-strand	142-144	3	23
α-helix	147-149	3
β-strand	153-155	3	23
β-strand	162-163	2	24
β-strand	165	1	25
α-helix	171	1
β-strand	172	1	25
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	297-301	5

Chain D: 10 helices, 66 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	26
β-strand	17-21	5	27
β-strand	30-35	6	27
β-strand	38-44	7	27
β-strand	49-56	8	27
β-strand	61-67	7	28
β-strand	76-81	6	28
β-strand	85-94	10	28
β-strand	97-107	11	28
β-strand	115	1	29
β-strand	121-124	4	30
β-strand	130-134	5	30
β-strand	136	1	29
β-strand	139-144	6	30
β-strand	155-158	4	30
β-strand	163-169	7	31
α-helix	170	1
β-strand	177-184	8	31
β-strand	187-196	10	31
β-strand	201-204	4	31
β-strand	210-211	2	31
β-strand	218-221	4	32
β-strand	229-232	4	32
β-strand	237-241	5	32
β-strand	244-248	5	32
α-helix	251-253	3
β-strand	258-263	6	33
β-strand	270-275	6	33
β-strand	279-289	11	33
β-strand	295-307	13	33
β-strand	313-318	6	34
β-strand	321-325	5	34
β-strand	331-336	6	34
β-strand	347-353	7	34
β-strand	359-365	7	35
β-strand	374-379	6	35
α-helix	382-384	3
β-strand	386-392	7	35
β-strand	710-716	7	35
β-strand	720-727	8	36
β-strand	732-743	12	36
β-strand	749-751	3	36
β-strand	762-765	4	36
α-helix	766-768	3
β-strand	785-795	11	36
β-strand	801-806	6	36
β-strand	811-819	9	37
β-strand	828-835	8	37
β-strand	846-854	9	37
β-strand	857-866	10	37
β-strand	870-876	7	38
β-strand	879-884	6	38
β-strand	887-893	7	38
β-strand	899-906	8	38
β-strand	913-917	5	39
β-strand	920-924	5	39
β-strand	929-936	8	39
β-strand	941-949	9	39
β-strand	954-959	6	40
β-strand	964-969	6	40
β-strand	973-978	6	40
β-strand	991	1	39
β-strand	993-999	7	40
β-strand	1004-1009	6	26
β-strand	1025-1032	8	26
β-strand	1037-1042	6	26
α-helix	1045-1061	17
α-helix	1070-1074	5
β-strand	1076-1077	2	41
β-strand	1082-1083	2	41
β-strand	1086	1	40
β-strand	1088-1090	3	26
α-helix	1091-1095	5
α-helix	1096-1099	4
α-helix	1102-1108	7
α-helix	1126-1137	12

Chain E: 16 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	58-60	3
α-helix	63-64	2
β-strand	65-66	2	42
α-helix	73-74	2
β-strand	78-83	6	42
α-helix	91-92	2
β-strand	96-101	6	42
α-helix	104-115	12
β-strand	119-127	9	42
β-strand	132-146	15	42
β-strand	155-167	13	42
β-strand	179-184	6	42
α-helix	185-186	2
β-strand	188	1	43
α-helix	200-205	6
α-helix	220-231	12
α-helix	233-237	5
α-helix	242-246	5
α-helix	250-262	13
α-helix	277-286	10
α-helix	292-299	8
β-strand	303	1	43
α-helix	304-317	14
β-strand	320-323	4	44
β-strand	330-333	4	44
α-helix	334-336	3
β-strand	337	1	45
β-strand	341	1	46
β-strand	344	1	46
β-strand	346-350	5	45
β-strand	356-362	7	45
β-strand	368-375	8	45
β-strand	384-391	8	45
β-strand	397-404	8	45
β-strand	413-418	6	45
α-helix	419-421	3
β-strand	422-425	4	44

Chain F: 17 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	12-13	2	47
β-strand	17-24	8	47
β-strand	29-36	8	47
β-strand	42-49	8	47
α-helix	57-67	11
α-helix	74-75	2
β-strand	76-82	7	47
β-strand	85-91	7	47
β-strand	96	1	48
α-helix	97-103	7
α-helix	110-129	20
β-strand	132-133	2	49
α-helix	139-141	3
β-strand	142-144	3	48
α-helix	147-149	3
β-strand	153-155	3	48
β-strand	162-163	2	49
β-strand	165	1	50
α-helix	171	1
β-strand	172	1	50
α-helix	173-175	3
α-helix	190-194	5
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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA damage-binding protein 1	A, D	protein	856	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

>5FQD_1 DNA DAMAGE-BINDING PROTEIN 1 (chains A, D)
MHHHHHHVDEENLYFQGGGRMSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLE
IYVVTAEGLRPVKEVGMYGKIAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDI
ITRAHGNVQDRIGRPSETGIIGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLE
ELHVIDVKFLYGCQAPTICFVYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVI
AVPEPFGGAIIIGQESITYHNGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRL
FMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDS
NEQGSYVVAMETFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGGNGNS
GEIQKLHIRTVPLYESPRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSS
VSSSKLFSSSTAPHETSFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKD
PNTYFIVGTAMVYPEEAEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASI
NSTVRLYEWTTEKELRTECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEE
IARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFV
NVFCHGSLVMQNLGETSTPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKS
VGKIEHSFWRSFHTERKTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREA
TADDLIKVVEELTRIH

Sequence of entity 2 (B, E), FASTA

>5FQD_2 PROTEIN CEREBLON (chains B, E)
MDWSHPQFEKSAVDENLYFQGGGRAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDD
SCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFG
TTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSA
VQLESLNKCQIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDR
IKKQLREWDENLKDDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMN
KCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPST
EHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPD
KVILCL

Sequence of entity 3 (C, F), FASTA

>5FQD_3 CASEIN KINASE I ISOFORM ALPHA (chains C, F)
GGGRMASSSGSKAEFIVGGKYKLVRKIGSGSFGDIYLAINITNGEEVAVKLESQKARHPQ
LLYESKLYKILQGGVGIPHIRWYGQEKDYNVLVMDLLGPSLEDLFNFCSRRFTMKTVLML
ADQMISRIEYVHTKNFIHRDIKPDNFLMGIGRHCNKLFLIDFGLAKKYRDNRTRQHIPYR
EDKNLTGTARYASINAHLGIEQSRRDDMESLGYVLMYFNRTSLPWQGLKAATKKQKYEKI
SEKKMSTPVEVLCKGFPAEFAMYLNYCRGLRFEEAPDYMYLRQLFRILFRTLNHQYDYTF
DWTMLKQKAAQQAASSSGQGQQAQTPTGKQTDKTKSNMKGF

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
LVY	S-Lenalidomide	C13 H13 N3 O3	2

Primary citation

Structural Basis of Lenalidomide-Induced Ck1Alpha Degradation by the Crl4(Crbn) Ubiquitin Ligase. Petzold, G., Fischer, E.S., Thoma, N.H. Nature (2016) 532:127. DOI 10.1038/NATURE16979 · 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

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