9BBE: Co-crystal structure of human DDB1

Co-crystal structure of human DDB1 bound to fragment UB028668. Determined by X-ray diffraction at 2.0 Å resolution. Released 12 Jun 2024.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 1
Atoms: 8,961
Mol. weight: 127.79 kDa
Ligands: A1AK9, TLA
Released: 12 Jun 2024

Explore 9BBE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9BBE contains 19 α-helices and 102 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: 19 helices, 102 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
α-helix	114	1
β-strand	115	1	4
α-helix	116	1
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	218-221	4	7
α-helix	222-223	2
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	279-289	11	8
β-strand	295-307	13	8
α-helix	310-311	2
β-strand	313-316	4	9
β-strand	321-325	5	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	394	1	11
β-strand	396-403	8	12
β-strand	409-413	5	13
β-strand	422	1	14
β-strand	424-429	6	13
β-strand	432-439	8	13
β-strand	442-446	5	13
β-strand	457-463	7	15
β-strand	467-472	6	15
β-strand	476-480	5	15
β-strand	486-490	5	15
α-helix	496-498	3
β-strand	500-503	4	16
β-strand	507-512	6	16
β-strand	515-522	8	16
β-strand	525-533	9	16
β-strand	538-542	5	17
β-strand	555-560	6	17
β-strand	565-570	6	17
β-strand	576-581	6	17
β-strand	588-596	9	18
β-strand	599-606	8	18
β-strand	610-616	7	18
β-strand	623-630	8	18
α-helix	635-636	2
β-strand	637-643	7	19
β-strand	646-652	7	19
β-strand	657-662	6	19
β-strand	665-670	6	19
β-strand	671	1	11
β-strand	678-682	5	12
β-strand	684	1	14
β-strand	690-694	5	12
β-strand	698-704	7	12
β-strand	710-716	7	10
β-strand	720-727	8	20
α-helix	728-730	3
β-strand	732-742	11	20
β-strand	750-751	2	20
α-helix	756-758	3
β-strand	762-765	4	20
β-strand	785-795	11	20
β-strand	801-806	6	20
β-strand	811-819	9	21
β-strand	828-835	8	21
β-strand	846-854	9	21
β-strand	857-866	10	21
β-strand	870-876	7	22
β-strand	879-884	6	22
β-strand	887-893	7	22
β-strand	899-905	7	22
β-strand	911-917	7	23
β-strand	920-925	6	23
β-strand	928	1	24
β-strand	930-936	7	23
β-strand	941-947	7	23
β-strand	952	1	24
β-strand	954-961	8	25
β-strand	964-969	6	25
β-strand	973-978	6	25
β-strand	991	1	23
β-strand	993-999	7	25
β-strand	1004-1009	6	1
β-strand	1024-1032	9	1
β-strand	1037-1043	7	1
α-helix	1045-1061	17
α-helix	1063-1064	2
α-helix	1065-1067	3
α-helix	1070-1074	5
β-strand	1076-1077	2	26
β-strand	1082-1083	2	26
β-strand	1086	1	25
β-strand	1088-1090	3	1
α-helix	1091-1095	5
α-helix	1096-1099	4
α-helix	1102-1109	8
β-strand	1113	1	27
β-strand	1123	1	27
α-helix	1126-1137	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA damage-binding protein 1	A	protein	1142	Homo sapiens	Q16531 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9BBE_1 DNA damage-binding protein 1 (chains A)
GSMSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMY
GKIAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSET
GIIGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTI
CFVYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESIT
YHNGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLK
DLRVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGP
IVDMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGIHEHASIDLPGIKGLWPLRSDPN
RETDDTLVLSFVGQTRVLMLNGEEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASVRL
VSQEPKALVSEWKEPQAKNISVASCNSSQVVVAVGRALYYLQIHPQELRQISHTEMEHEV
ACLDITPLGDSNGLSPLCAIGLWTDISARILKLPSFELLHKEMLGGEIIPRSILMTTFES
SHYLLCALGDGALFYFGLNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTV
IYSSNHKLVFSNVNLKEVNYMCPLNSDGYPDSLALANNSTLTIGTIDEIQKLHIRTVPLY
ESPRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPH
ETSFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYP
EEAEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKE
LRTECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVE
ILDDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLG
ETSTPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHT
ERKTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTR
IH

Ligands and cofactors

ID	Name	Formula	Copies
A1AK9	5-(4-methoxyphenyl)-3-[(3S)-pyrrolidin-3-yl]-1,2,4-oxadiazole	C13 H15 N3 O2	1
TLA	L(+)-tartaric acid	C4 H6 O6	2

Water and common crystallization additives (UNX) are not listed.

Primary citation

Co-crystal structure of human DDB1 bound to fragment UB028668. Zeng, H., Dong, A., Frommlet, A. et al. To be published.

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
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
3EI3 2.3 Å, Structure of the hsDDB1-drDDB2 complex

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