3I7P: DDB1

Crystal Structure of DDB1 in Complex with the H-Box Motif of WDR40A. Determined by X-ray diffraction at 3.0 Å resolution. Released 8 Dec 2009.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 2
Atoms: 8,842
Mol. weight: 129.06 kDa
Released: 8 Dec 2009

Explore 3I7P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3I7P contains 13 α-helices and 102 β-strands across 2 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, 102 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	1
β-strand	17-21	5	2
β-strand	30-34	5	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	164-169	6	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	218-220	3	7
β-strand	229-232	4	7
β-strand	237-241	5	7
β-strand	244-248	5	7
α-helix	251-254	4
β-strand	258-263	6	8
β-strand	270-275	6	8
β-strand	279-290	12	8
β-strand	293-307	15	8
β-strand	313-316	4	9
β-strand	321-325	5	9
β-strand	331-341	11	9
β-strand	345-353	9	9
β-strand	359-365	7	10
α-helix	373	1
β-strand	374-379	6	10
α-helix	382-384	3
β-strand	386-392	7	10
β-strand	394	1	11
β-strand	396	1	12
β-strand	402	1	13
β-strand	427-428	2	14
β-strand	433-434	2	14
β-strand	437-438	2	15
β-strand	443-444	2	15
β-strand	457-459	3	16
β-strand	467-472	6	16
β-strand	476-480	5	16
β-strand	489	1	16
β-strand	507-508	2	17
β-strand	516	1	18
β-strand	519-522	4	17
β-strand	525-528	4	17
β-strand	532	1	18
β-strand	538-542	5	19
β-strand	556-560	5	19
β-strand	565-569	5	19
β-strand	576-580	5	19
β-strand	590-595	6	20
β-strand	600-605	6	20
β-strand	611-615	5	20
β-strand	628	1	20
β-strand	637-640	4	21
β-strand	649-652	4	21
β-strand	657-659	3	21
β-strand	668-670	3	21
β-strand	671	1	11
β-strand	678-684	7	13
β-strand	687-695	9	13
β-strand	698-701	4	13
β-strand	704	1	12
β-strand	710-716	7	10
β-strand	720-727	8	22
β-strand	732-742	11	22
β-strand	743	1	23
β-strand	749	1	23
β-strand	764-765	2	22
β-strand	785-795	11	22
β-strand	801-806	6	22
β-strand	811-820	10	24
β-strand	827-835	9	24
β-strand	846-847	2	25
β-strand	848-853	6	24
β-strand	858-862	5	24
β-strand	865-866	2	25
β-strand	872-875	4	26
β-strand	880-885	6	26
β-strand	887-893	7	26
β-strand	899-905	7	26
β-strand	916-917	2	27
β-strand	921-923	3	27
β-strand	931-936	6	27
β-strand	941-947	7	27
β-strand	954-959	6	28
β-strand	965-969	5	28
β-strand	973-979	7	28
β-strand	991	1	27
β-strand	992-999	8	28
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	1065-1067	3
α-helix	1070-1073	4
β-strand	1078	1	29
β-strand	1081	1	29
β-strand	1086	1	28
β-strand	1090	1	1
α-helix	1091-1094	4
α-helix	1095-1099	5
α-helix	1102-1106	5
α-helix	1129-1132	4
α-helix	1134-1137	4

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	47-55	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA damage-binding protein 1	A	protein	1143	Homo sapiens	Q16531 (AlphaFold model)
WD repeat-containing protein 40A	B	protein	13	Homo sapiens	Q5T6F0 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3I7P_1 DNA damage-binding protein 1 (chains A)
GSHMSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGM
YGKIAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSE
TGIIGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPT
ICFVYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESI
TYHNGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTL
KDLRVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLG
PIVDMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGIHEHASIDLPGIKGLWPLRSDP
NRETYDTLVLSFVGQTRVLMLNGEEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASVR
LVSQEPKALVSEWKEPQAKNISVASCNSSQVVVAVGRALYYLQIHPQELRQISHTEMEHE
VACLDITPLGDSNGLSPLCAIGLWTDISARILKLPSFELLHKEMLGGEIIPRSILMTTFE
SSHYLLCALGDGALFYFGLNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPT
VIYSSNHKLVFSNVNLKEVNYMCPLNSDGYPDSLALANNSTLTIGTIDEIQKLHIRTVPL
YESPRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAP
HETSFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVY
PEEAEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEK
DVRTECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAV
EILDDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNL
GETSTPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFH
TERKTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELT
RIH

Sequence of entity 2 (B), FASTA

>3I7P_2 WD repeat-containing protein 40A (chains B)
SLVYYLKNREVRL

Primary citation

A promiscuous alpha-helical motif anchors viral hijackers and substrate receptors to the CUL4-DDB1 ubiquitin ligase machinery. Li, T., Robert, E.I., van Breugel, P.C. et al. Nat Struct Mol Biol (2010) 17:105-111. DOI 10.1038/nsmb.1719 · 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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