3E0C: DNA Damage-Binding protein 1(DDB1)

Crystal Structure of DNA Damage-Binding protein 1(DDB1). Determined by X-ray diffraction at 2.41 Å resolution. Released 16 Sept 2008.

Method: X-ray diffraction
Resolution: 2.41 Å
Organism: Homo sapiens
Chains: 1
Atoms: 7,777
Mol. weight: 127.1 kDa
Released: 16 Sept 2008

Explore 3E0C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3E0C contains 15 α-helices and 95 β-strands across 1 chain. 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: 15 helices, 95 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	1
β-strand	17-21	5	2
α-helix	28-29	2
β-strand	30-35	6	2
β-strand	38-43	6	2
β-strand	50-56	7	2
β-strand	61-67	7	3
β-strand	76-81	6	3
β-strand	85-91	7	3
β-strand	100-107	8	3
β-strand	121-124	4	4
β-strand	130-136	7	4
β-strand	139-144	6	4
β-strand	155-158	4	4
β-strand	164-169	6	5
β-strand	177-182	6	5
β-strand	189-196	8	5
β-strand	201-204	4	5
β-strand	218-221	4	6
β-strand	229-232	4	6
β-strand	237-240	4	6
β-strand	247-248	2	6
α-helix	251-253	3
β-strand	258-263	6	7
β-strand	270-275	6	7
β-strand	279-286	8	7
β-strand	299-307	9	7
β-strand	311-316	6	8
β-strand	321-326	6	8
β-strand	331-336	6	8
β-strand	347-353	7	8
β-strand	359-365	7	9
β-strand	374-379	6	9
α-helix	382-384	3
β-strand	386-392	7	9
β-strand	394	1	10
β-strand	396-403	8	11
β-strand	409-413	5	12
β-strand	424-429	6	12
β-strand	432-437	6	12
β-strand	446	1	12
β-strand	457-463	7	13
β-strand	467-472	6	13
β-strand	476-480	5	13
β-strand	486-490	5	13
α-helix	496-498	3
β-strand	500-503	4	14
β-strand	507-512	6	14
β-strand	515-522	8	14
β-strand	525-533	9	14
β-strand	538-542	5	15
β-strand	555-560	6	15
β-strand	565-570	6	15
β-strand	576-581	6	15
α-helix	586-587	2
β-strand	588-596	9	16
β-strand	599-606	8	16
β-strand	610-616	7	16
β-strand	623-624	2	16
β-strand	628-630	3	16
α-helix	635-636	2
β-strand	637-642	6	17
β-strand	647-652	6	17
β-strand	657-660	4	17
β-strand	667-670	4	17
β-strand	671	1	10
β-strand	678-681	4	11
β-strand	691-694	4	11
β-strand	698-704	7	11
β-strand	710-716	7	9
β-strand	720-727	8	18
α-helix	728-730	3
β-strand	732-740	9	18
α-helix	756-758	3
β-strand	762-765	4	18
β-strand	787-795	9	18
β-strand	801-806	6	18
β-strand	811-819	9	19
β-strand	828-835	8	19
β-strand	846-852	7	19
β-strand	859-866	8	19
β-strand	870-876	7	20
β-strand	879-884	6	20
β-strand	887-893	7	20
β-strand	899-905	7	20
β-strand	911-917	7	21
β-strand	920-925	6	21
β-strand	928	1	22
β-strand	930-936	7	21
β-strand	941-947	7	21
β-strand	952	1	22
β-strand	954-961	8	23
β-strand	964-969	6	23
β-strand	973-977	5	23
β-strand	991	1	21
β-strand	994-999	6	23
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	1063-1064	2
α-helix	1070-1073	4
β-strand	1076	1	24
β-strand	1083	1	24
β-strand	1086	1	23
β-strand	1088-1090	3	1
α-helix	1091-1095	5
α-helix	1096-1098	3
α-helix	1102-1109	8
α-helix	1126-1137	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA damage-binding protein 1	A	protein	1140	Homo sapiens	Q16531 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3E0C_1 DNA damage-binding protein 1 (chains A)
MSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGK
IAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGI
IGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICF
VYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYH
NGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDL
RVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIV
DMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGIHEHASIDLPGIKGLWPLRSDPNRE
TDDTLVLSFVGQTRVLMLNGEEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVS
QEPKALVSEWKEPQAKNISVASCNSSQVVVAVGRALYYLQIHPQELRQISHTEMEHEVAC
LDITPLGDSNGLSPLCAIGLWTDISARILKLPSFELLHKEMLGGEIIPRSILMTTFESSH
YLLCALGDGALFYFGLNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTVIY
SSNHKLVFSNVNLKEVNYMCPLNSDGYPDSLALANNSTLTIGTIDEIQKLHIRTVPLYES
PRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHET
SFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEE
AEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELR
TECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEIL
DDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGET
STPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTER
KTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH

Primary citation

Structure and function of WD40 domain proteins. Xu, C., Min, J. Protein Cell (2011) 2:202-214. DOI 10.1007/s13238-011-1018-1 · 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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