6H0F: DDB1-CRBN-pomalidomide complex

Structure of DDB1-CRBN-pomalidomide complex bound to IKZF1(ZF2). Determined by X-ray diffraction at 3.25 Å resolution. Released 7 Nov 2018.

Method: X-ray diffraction
Resolution: 3.25 Å
Organism: Homo sapiens
Chains: 12
Atoms: 39,004
Mol. weight: 597.39 kDa
Ligands: ZN, Y70
Released: 7 Nov 2018

Explore 6H0F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6H0F contains 139 α-helices and 357 β-strands across 12 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: 16 helices, 70 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
α-helix	222-223	2
β-strand	229-232	4	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	279-288	10	8
β-strand	296-307	12	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	361-365	5	10
β-strand	372	1	11
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	12
β-strand	732-743	12	12
β-strand	749-751	3	12
β-strand	762-765	4	12
α-helix	770-773	4
α-helix	780-781	2
β-strand	785-795	11	12
β-strand	801-806	6	12
β-strand	811-819	9	13
β-strand	828-835	8	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	899-906	8	14
β-strand	913-917	5	15
β-strand	920-924	5	15
β-strand	929-936	8	15
β-strand	941-949	9	15
β-strand	954-959	6	16
β-strand	964-969	6	16
β-strand	973-979	7	16
α-helix	980	1
α-helix	986-989	4
β-strand	991	1	15
β-strand	992-999	8	16
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	1065-1067	3
α-helix	1070-1074	5
β-strand	1076-1077	2	17
β-strand	1082-1083	2	17
β-strand	1086	1	16
β-strand	1088-1090	3	1
α-helix	1091-1095	5
α-helix	1096-1099	4
α-helix	1102-1108	7
β-strand	1113-1115	3	18
β-strand	1121-1123	3	18
α-helix	1124	1
α-helix	1126-1137	12

Chain B: 17 helices, 19 β-strands

Element	Residues	Length	Sheet
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	152-169	18	19
β-strand	172	1	19
β-strand	178-185	8	19
α-helix	186	1
β-strand	188	1	20
α-helix	200-203	4
α-helix	204-206	3
α-helix	215-219	5
α-helix	221-231	11
α-helix	233-237	5
α-helix	242-246	5
α-helix	250-264	15
α-helix	269-272	4
α-helix	277-287	11
α-helix	292-300	9
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	422-425	4	21
α-helix	426-428	3

Chains C, F and I: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	145-146	2	23
β-strand	153-154	2	23
α-helix	157-168	12

Chain D: 15 helices, 68 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	24
β-strand	17-21	5	25
β-strand	30-35	6	25
β-strand	38-44	7	25
β-strand	49-56	8	25
β-strand	61-67	7	26
β-strand	76-81	6	26
β-strand	85-94	10	26
β-strand	97-107	11	26
β-strand	115	1	27
β-strand	121-124	4	28
β-strand	130-134	5	28
β-strand	136	1	27
β-strand	139-144	6	28
β-strand	155-158	4	28
β-strand	163-169	7	29
α-helix	170	1
β-strand	177-184	8	29
β-strand	187-196	10	29
β-strand	201-204	4	29
β-strand	210-211	2	29
β-strand	218-221	4	30
α-helix	222-223	2
β-strand	229-232	4	30
β-strand	237-241	5	30
β-strand	244-248	5	30
α-helix	251-253	3
β-strand	258-263	6	31
β-strand	270-275	6	31
β-strand	279-288	10	31
β-strand	296-307	12	31
β-strand	311-316	6	32
β-strand	321-326	6	32
β-strand	331-336	6	32
β-strand	347-353	7	32
β-strand	361-365	5	33
β-strand	372	1	34
β-strand	374-379	6	33
α-helix	382-384	3
β-strand	386-392	7	33
β-strand	710-716	7	33
β-strand	720-727	8	35
β-strand	732-743	12	35
β-strand	749-751	3	35
β-strand	762-765	4	35
α-helix	770-773	4
α-helix	780-781	2
β-strand	785-795	11	35
β-strand	801-806	6	35
β-strand	811-819	9	36
β-strand	828-835	8	36
β-strand	846-854	9	36
β-strand	857-866	10	36
β-strand	870-876	7	37
β-strand	879-884	6	37
β-strand	887-893	7	37
β-strand	899-906	8	37
β-strand	913-917	5	38
β-strand	920-924	5	38
β-strand	929-936	8	38
β-strand	941-949	9	38
β-strand	954-959	6	39
β-strand	964-969	6	39
β-strand	973-979	7	39
α-helix	980	1
α-helix	986-989	4
β-strand	991	1	38
β-strand	992-999	8	39
β-strand	1004-1009	6	24
β-strand	1014	1	34
β-strand	1025-1032	8	24
β-strand	1037-1042	6	24
α-helix	1045-1061	17
α-helix	1065-1067	3
α-helix	1070-1074	5
β-strand	1076-1077	2	40
β-strand	1082-1083	2	40
β-strand	1086	1	39
β-strand	1089-1090	2	24
α-helix	1091-1095	5
α-helix	1096-1099	4
α-helix	1102-1108	7
α-helix	1126-1137	12

Chain E: 20 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	73-74	2
β-strand	78-83	6	41
β-strand	96-101	6	41
α-helix	104-115	12
β-strand	119-127	9	41
β-strand	132-149	18	41
β-strand	152-169	18	41
α-helix	171	1
β-strand	172	1	41
α-helix	173	1
β-strand	178-185	8	41
α-helix	186	1
β-strand	188	1	42
α-helix	200-203	4
α-helix	204-206	3
α-helix	215-219	5
α-helix	221-231	11
α-helix	233-237	5
α-helix	242-246	5
α-helix	250-264	15
α-helix	269-272	4
α-helix	277-287	11
α-helix	292-300	9
β-strand	303	1	42
α-helix	304-316	13
β-strand	320-323	4	43
β-strand	330-333	4	43
α-helix	334-336	3
β-strand	337	1	44
β-strand	346-350	5	44
β-strand	356-362	7	44
β-strand	368-375	8	44
β-strand	384-391	8	44
β-strand	397-404	8	44
β-strand	413-418	6	44
α-helix	419-421	3
β-strand	422-425	4	43
α-helix	426-428	3
α-helix	436-438	3

Chain G: 16 helices, 68 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	46
β-strand	17-21	5	47
β-strand	30-35	6	47
β-strand	38-44	7	47
β-strand	49-56	8	47
β-strand	61-67	7	48
β-strand	76-81	6	48
β-strand	85-94	10	48
β-strand	97-107	11	48
β-strand	115	1	49
β-strand	121-124	4	50
β-strand	130-134	5	50
β-strand	136	1	49
β-strand	139-144	6	50
β-strand	155-158	4	50
β-strand	163-169	7	51
α-helix	170	1
β-strand	177-184	8	51
β-strand	187-196	10	51
β-strand	201-204	4	51
β-strand	210-211	2	51
β-strand	218-221	4	30
α-helix	222-223	2
β-strand	229-232	4	30
β-strand	237-241	5	30
β-strand	244-248	5	30
α-helix	251-253	3
β-strand	258-263	6	52
β-strand	270-275	6	52
β-strand	279-288	10	52
β-strand	296-307	12	52
β-strand	311-318	8	53
β-strand	321-326	6	53
β-strand	331-336	6	53
α-helix	340-341	2
β-strand	347-353	7	53
β-strand	361-365	5	54
β-strand	372	1	55
β-strand	374-379	6	54
α-helix	382-384	3
β-strand	386-392	7	54
β-strand	710-716	7	54
β-strand	720-727	8	56
β-strand	732-743	12	56
β-strand	749-751	3	56
β-strand	762-765	4	56
α-helix	770-773	4
α-helix	780-781	2
β-strand	785-795	11	56
β-strand	801-806	6	56
β-strand	811-819	9	57
β-strand	828-835	8	57
β-strand	846-854	9	57
β-strand	857-866	10	57
β-strand	870-876	7	58
β-strand	879-884	6	58
β-strand	887-893	7	58
β-strand	899-906	8	58
β-strand	913-917	5	59
β-strand	920-924	5	59
β-strand	929-936	8	59
β-strand	941-949	9	59
β-strand	954-959	6	60
β-strand	964-969	6	60
β-strand	973-979	7	60
α-helix	980	1
α-helix	986-989	4
β-strand	991	1	59
β-strand	992-999	8	60
β-strand	1004-1009	6	46
β-strand	1014	1	55
β-strand	1025-1032	8	46
β-strand	1037-1042	6	46
α-helix	1045-1061	17
α-helix	1065-1067	3
α-helix	1070-1074	5
β-strand	1076-1077	2	61
β-strand	1082-1083	2	61
β-strand	1086	1	60
β-strand	1088-1090	3	46
α-helix	1091-1095	5
α-helix	1096-1099	4
α-helix	1102-1108	7
α-helix	1126-1137	12

Chain H: 19 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	73-74	2
β-strand	78-83	6	62
β-strand	96-101	6	62
α-helix	104-115	12
β-strand	119-127	9	62
β-strand	132-149	18	62
β-strand	152-169	18	62
α-helix	171	1
β-strand	172	1	62
α-helix	173	1
β-strand	178-185	8	62
α-helix	186	1
β-strand	188	1	63
α-helix	200-203	4
α-helix	215-219	5
α-helix	221-231	11
α-helix	233-237	5
α-helix	242-246	5
α-helix	250-264	15
α-helix	269-272	4
α-helix	277-287	11
α-helix	292-300	9
β-strand	303	1	63
α-helix	304-316	13
β-strand	320-323	4	64
β-strand	330-333	4	64
α-helix	334-336	3
β-strand	337	1	65
β-strand	346-350	5	65
β-strand	356-362	7	65
β-strand	368-375	8	65
β-strand	384-391	8	65
β-strand	397-404	8	65
β-strand	413-418	6	65
α-helix	419-421	3
β-strand	422-425	4	64
α-helix	426-428	3
α-helix	436-438	3

Chain J: 15 helices, 68 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	67
β-strand	17-21	5	68
β-strand	30-35	6	68
β-strand	38-44	7	68
β-strand	49-56	8	68
β-strand	61-67	7	69
β-strand	76-81	6	69
β-strand	85-94	10	69
β-strand	97-107	11	69
β-strand	115	1	70
β-strand	121-124	4	71
β-strand	130-134	5	71
β-strand	136	1	70
β-strand	139-144	6	71
β-strand	155-158	4	71
β-strand	163-169	7	72
α-helix	170	1
β-strand	177-184	8	72
β-strand	187-196	10	72
β-strand	201-204	4	72
β-strand	210-211	2	72
β-strand	218-221	4	7
α-helix	222-223	2
β-strand	229-232	4	7
β-strand	237-241	5	7
β-strand	244-248	5	7
α-helix	251-253	3
β-strand	258-263	6	73
β-strand	270-275	6	73
β-strand	279-288	10	73
β-strand	296-307	12	73
β-strand	311-318	8	74
β-strand	321-326	6	74
β-strand	331-336	6	74
β-strand	347-353	7	74
β-strand	361-365	5	75
β-strand	374-379	6	75
α-helix	382-384	3
β-strand	386-390	5	75
α-helix	708-710	3
β-strand	713-716	4	75
β-strand	720-727	8	76
β-strand	732-743	12	76
β-strand	749-751	3	76
β-strand	762-765	4	76
α-helix	770-773	4
α-helix	780-781	2
β-strand	785-795	11	76
β-strand	801-806	6	76
β-strand	811-819	9	77
β-strand	828-835	8	77
β-strand	846-854	9	77
β-strand	857-866	10	77
β-strand	870-876	7	78
β-strand	879-884	6	78
β-strand	887-893	7	78
β-strand	899-906	8	78
β-strand	913-917	5	79
β-strand	920-924	5	79
β-strand	929-936	8	79
β-strand	941-949	9	79
β-strand	954-959	6	80
β-strand	964-969	6	80
β-strand	973-979	7	80
α-helix	986-989	4
β-strand	991	1	79
β-strand	992-999	8	80
β-strand	1004-1009	6	67
β-strand	1025-1032	8	67
β-strand	1037-1042	6	67
α-helix	1045-1061	17
α-helix	1065-1067	3
α-helix	1070-1074	5
β-strand	1076-1077	2	81
β-strand	1082-1083	2	81
β-strand	1086	1	80
β-strand	1088-1090	3	67
α-helix	1091-1095	5
α-helix	1096-1099	4
α-helix	1102-1108	7
β-strand	1113-1115	3	82
β-strand	1121-1123	3	82
α-helix	1126-1137	12

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1,DNA…	A, D, G, J	protein	856	Homo sapiens	Q16531 (AlphaFold model)
Protein cereblon	B, E, H, K	protein	426	Homo sapiens	Q96SW2 (AlphaFold model)
DNA-binding protein Ikaros	C, F, I, L	protein	38	Homo sapiens	Q13422 (AlphaFold model)

Sequence of entity 1 (A, D, G, J), FASTA

>6H0F_1 DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1 (chains A, D, G, J)
MHHHHHHVDEENLYFQGGGRMSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLE
IYVVTAEGLRPVKEVGMYGKIAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDI
ITRAHGNVQDRIGRPSETGIIGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLE
ELHVIDVKFLYGCQAPTICFVYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVI
AVPEPFGGAIIIGQESITYHNGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRL
FMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDS
NEQGSYVVAMETFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGGNGNS
GEIQKLHIRTVPLYESPRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSS
VSSSKLFSSSTAPHETSFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKD
PNTYFIVGTAMVYPEEAEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASI
NSTVRLYEWTTEKELRTECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEE
IARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFV
NVFCHGSLVMQNLGETSTPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKS
VGKIEHSFWRSFHTERKTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREA
TADDLIKVVEELTRIH

Sequence of entity 2 (B, E, H, K), FASTA

>6H0F_2 Protein cereblon (chains B, E, H, K)
MDWSHPQFEKSAVDENLYFQGGGRAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDD
SCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFG
TTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSA
VQLESLNKCQIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDR
IKKQLREWDENLKDDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMN
KCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPST
EHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPD
KVILCL

Sequence of entity 3 (C, F, I, L), FASTA

>6H0F_3 DNA-binding protein Ikaros (chains C, F, I, L)
GGGRGERPFQCNQCGASFTQKGNLLRHIKLHSGEKPFK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8
Y70	S-Pomalidomide	C13 H11 N3 O4	4

Primary citation

Defining the human C2H2 zinc finger degrome targeted by thalidomide analogs through CRBN. Sievers, Q.L., Petzold, G., Bunker, R.D. et al. Science (2018) 362:eaat0572. DOI 10.1126/science.aat0572 · 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

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