2B5L: DDB1

Crystal Structure of DDB1 In Complex with Simian Virus 5 V Protein. Determined by X-ray diffraction at 2.85 Å resolution. Released 28 Feb 2006.

Method: X-ray diffraction
Resolution: 2.85 Å
Organisms: Homo sapiens, Simian virus 5
Chains: 4
Atoms: 20,399
Mol. weight: 302.43 kDa
Ligands: ZN
Released: 28 Feb 2006

Explore 2B5L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2B5L contains 37 α-helices and 235 β-strands across 4 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: 13 helices, 106 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	85-93	9	3
β-strand	98-107	10	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	187-194	8	6
β-strand	195-196	2	7
β-strand	201-202	2	7
β-strand	209	1	6
β-strand	218-221	4	8
α-helix	222-223	2
β-strand	229-232	4	8
β-strand	237-241	5	8
β-strand	244-248	5	8
α-helix	251-254	4
β-strand	260-265	6	9
β-strand	268-274	7	9
β-strand	279-289	11	9
β-strand	295-307	13	9
β-strand	311-316	6	10
β-strand	321-326	6	10
β-strand	331-336	6	10
β-strand	347-353	7	10
β-strand	359-364	6	11
β-strand	375-379	5	11
α-helix	382-384	3
β-strand	386-391	6	11
β-strand	394	1	12
β-strand	396-402	7	13
β-strand	409-413	5	14
β-strand	424-428	5	14
β-strand	433-439	7	14
β-strand	442-446	5	14
β-strand	457-463	7	15
β-strand	467-472	6	15
β-strand	476-479	4	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	575-581	7	17
α-helix	587	1
β-strand	588-595	8	18
β-strand	600-606	7	18
β-strand	610-616	7	18
β-strand	623-630	8	18
β-strand	637-641	5	19
β-strand	648-652	5	19
β-strand	657-661	5	19
β-strand	666-670	5	19
β-strand	671	1	12
β-strand	678-682	5	13
β-strand	690-694	5	13
β-strand	699-704	6	13
β-strand	711-716	6	11
β-strand	720-724	5	20
β-strand	727	1	20
β-strand	732-742	11	20
β-strand	743	1	21
β-strand	749	1	21
β-strand	765	1	20
β-strand	785-795	11	20
β-strand	801-806	6	20
α-helix	807-808	2
β-strand	811-815	5	22
β-strand	818-821	4	22
β-strand	824-835	12	22
β-strand	846-847	2	23
β-strand	848-855	8	22
β-strand	857-862	6	22
β-strand	865-866	2	23
β-strand	872-876	5	24
β-strand	879-883	5	24
β-strand	888-893	6	24
β-strand	899-905	7	24
β-strand	911-917	7	25
β-strand	920-925	6	25
β-strand	928	1	26
β-strand	930-936	7	25
β-strand	941-947	7	25
β-strand	952	1	26
β-strand	954-961	8	27
β-strand	964-969	6	27
β-strand	973-979	7	27
β-strand	991	1	25
β-strand	992-999	8	27
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	1070-1073	4
β-strand	1076-1077	2	28
β-strand	1082-1083	2	28
β-strand	1086	1	27
β-strand	1088-1090	3	1
α-helix	1091-1096	6
α-helix	1097-1099	3
α-helix	1102-1109	8
β-strand	1113-1114	2	29
β-strand	1122-1123	2	29
α-helix	1126-1137	12

Chain B: 17 helices, 106 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	30
β-strand	17-21	5	31
β-strand	30-34	5	31
β-strand	38-44	7	31
β-strand	49-56	8	31
β-strand	61-67	7	32
β-strand	76-81	6	32
β-strand	85-91	7	32
β-strand	94	1	33
β-strand	97	1	33
β-strand	100-107	8	32
α-helix	114	1
β-strand	115	1	34
α-helix	116	1
β-strand	121-124	4	35
β-strand	130-134	5	35
β-strand	136	1	34
β-strand	141-144	4	35
β-strand	155	1	35
β-strand	163-166	4	36
β-strand	169	1	36
α-helix	170	1
β-strand	177-183	7	36
β-strand	188-194	7	36
β-strand	211	1	36
β-strand	216-220	5	37
β-strand	230-233	4	37
β-strand	236-239	4	37
β-strand	248	1	37
β-strand	260-263	4	38
β-strand	271-274	4	38
β-strand	279-280	2	38
β-strand	283-289	7	39
β-strand	295-302	8	39
β-strand	306-307	2	38
β-strand	313-316	4	40
β-strand	321-325	5	40
β-strand	331-336	6	40
α-helix	342-344	3
β-strand	347-353	7	40
β-strand	359-365	7	41
β-strand	374-379	6	41
α-helix	382-384	3
β-strand	386-393	8	41
β-strand	394	1	42
β-strand	396-405	10	43
β-strand	409-413	5	44
β-strand	424-428	5	44
β-strand	435-437	3	44
β-strand	459-463	5	45
β-strand	467-471	5	45
β-strand	476-480	5	45
β-strand	500-503	4	46
β-strand	507-511	5	46
β-strand	515-522	8	46
β-strand	525-533	9	46
β-strand	538-542	5	47
β-strand	555-560	6	47
β-strand	565-570	6	47
β-strand	578-581	4	47
α-helix	587	1
β-strand	588-595	8	48
β-strand	600-606	7	48
β-strand	610-616	7	48
β-strand	623-630	8	48
β-strand	637-641	5	49
β-strand	648-652	5	49
β-strand	657-661	5	49
β-strand	666-670	5	49
β-strand	671	1	42
β-strand	678-680	3	43
β-strand	683	1	50
β-strand	689	1	50
β-strand	691-695	5	43
β-strand	697-704	8	43
β-strand	709-716	8	41
β-strand	720-727	8	51
α-helix	728-730	3
β-strand	732-742	11	51
α-helix	743-744	2
β-strand	751	1	51
α-helix	756-758	3
β-strand	762-764	3	51
β-strand	785-795	11	51
β-strand	801-806	6	51
β-strand	811-819	9	52
β-strand	828-835	8	52
β-strand	846-847	2	53
β-strand	848-852	5	52
β-strand	859-860	2	52
β-strand	865-866	2	53
β-strand	872-876	5	54
β-strand	879-883	5	54
β-strand	888-893	6	54
β-strand	899-905	7	54
β-strand	911-917	7	55
β-strand	920-925	6	55
β-strand	928	1	56
β-strand	930-936	7	55
β-strand	941-947	7	55
β-strand	952	1	56
β-strand	954-959	6	57
β-strand	964-969	6	57
β-strand	973-978	6	57
α-helix	985-988	4
β-strand	991	1	55
α-helix	992	1
β-strand	993-999	7	57
β-strand	1004-1009	6	30
β-strand	1025-1032	8	30
β-strand	1038-1042	5	30
α-helix	1045-1061	17
α-helix	1070-1074	5
β-strand	1077	1	58
β-strand	1082	1	58
β-strand	1086	1	57
β-strand	1090	1	30
α-helix	1091-1095	5
α-helix	1096-1099	4
α-helix	1102-1107	6
β-strand	1113-1114	2	59
β-strand	1122-1123	2	59
α-helix	1126-1136	11

Chain C: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	18-19	2	60
α-helix	23-32	10
β-strand	42-43	2	60
β-strand	48	1	61
β-strand	95-97	3	62
α-helix	98-100	3
β-strand	111-116	6	61
β-strand	124	1	61
α-helix	127-138	12
β-strand	143-146	4	61
β-strand	171-178	8	61
β-strand	183-192	10	61
β-strand	202-204	3	62

Chain D: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	63
α-helix	24-33	10
β-strand	42	1	63
β-strand	47-49	3	64
β-strand	83	1	64
β-strand	95-97	3	65
α-helix	98	1
β-strand	111-115	5	64
β-strand	124	1	64
α-helix	127-137	11
β-strand	144-146	3	64
β-strand	171	1	66
β-strand	173-180	8	64
β-strand	183-189	7	64
β-strand	192	1	66
β-strand	202-204	3	65
α-helix	205-206	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
damage-specific DNA binding protein 1	A, B	protein	1140	Homo sapiens	Q16531 (AlphaFold model)
Nonstructural protein V	C, D	protein	222	Simian virus 5	P11207 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2B5L_1 damage-specific DNA binding protein 1 (chains A, B)
MSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGK
IAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGI
IGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICF
VYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYH
NGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDL
RVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIV
DMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGIHEHASIDLPGIKGLWPLRSDPNRE
TYDTLVLSFVGQTRVLMLNGEEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVS
QEPKALVSEWKEPQAKNISVASCNSSQVVVAVGRALYYLQIHPQELRQISHTEMEHEVAC
LDITPLGDSNGLSPLCAIGLWTDISARILKLPSFELLHKEMLGGEIIPRSILMTTFESSH
YLLCALGDGALFYFGLNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTVIY
SSNHKLVFSNVNLKEVNYMCPLNSDGYPDSLALANNSTLTIGTIDEIQKLHIRTVPLYES
PRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHET
SFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEE
AEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKDVR
TECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEIL
DDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGET
STPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTER
KTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH

Sequence of entity 2 (C, D), FASTA

>2B5L_2 Nonstructural protein V (chains C, D)
MDPTDLSFSPDEINKLIETGLNTVEYFTSQQVTGTSSLGKNTIPPGVTGLLTNAAEAKIQ
ESTNHQKGSVGGGAKPKKPRPKIAIVPADDKTVPGKPIPNPLLGLDSTPSTQTVLDLSGK
TLPSGSYKGVKLAKFGKENLMTRFIEEPRENPIATSSPIDFKRGRDTGGFHRREYSIGWV
GDEVKVTEWCNPSCSPITAAARRFECTCHQCPVTCSECERDT

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Primary citation

Structure of DDB1 in complex with a paramyxovirus V protein: viral hijack of a propeller cluster in ubiquitin ligase. Li, T., Chen, X., Garbutt, K.C. et al. Cell (2006) 124:105-117. DOI 10.1016/j.cell.2005.10.033 · 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

About this viewer

MolViewer shows 2B5L directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.