3DKB: A20, 2.5 angstrom

Crystal Structure of A20, 2.5 angstrom. Determined by X-ray diffraction at 2.5 Å resolution. Released 8 Jul 2008.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 6
Atoms: 17,550
Mol. weight: 274.02 kDa
Released: 8 Jul 2008

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

Secondary structure: helices and β-sheets

3DKB contains 126 α-helices and 120 β-strands across 6 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: 21 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	6010-6014	5
α-helix	6015-6027	13
β-strand	6029-6030	2	1
α-helix	6037-6038	2
β-strand	6039-6040	2	1
α-helix	6043-6045	3
β-strand	6050	1	2
α-helix	6051-6052	2
α-helix	6058-6068	11
β-strand	6069	1	3
α-helix	6071-6079	9
β-strand	6089	1	4
β-strand	6092-6094	3	5
β-strand	6095	1	3
α-helix	6096	1
α-helix	6103-6113	11
α-helix	6121-6132	12
α-helix	6136-6147	12
α-helix	6166-6174	9
α-helix	6178-6180	3
α-helix	6193-6202	10
β-strand	6207-6211	5	6
β-strand	6231-6233	3	6
β-strand	6248-6252	5	6
β-strand	6257-6259	3	6
β-strand	6260-6262	3	5
β-strand	6263	1	2
β-strand	6270	1	4
β-strand	6272-6274	3	7
β-strand	6276-6278	3	8
β-strand	6283-6285	3	8
α-helix	6286-6287	2
β-strand	6288	1	6
α-helix	6293-6297	5
α-helix	6299-6306	8
β-strand	6309-6315	7	7
β-strand	6322-6329	8	7
α-helix	6330-6331	2
α-helix	6337-6339	3
α-helix	6341-6357	17
α-helix	6359-6361	3

Chain B: 21 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	1010-1014	5
α-helix	1015-1027	13
β-strand	1029-1030	2	9
α-helix	1037-1038	2
β-strand	1039-1040	2	9
α-helix	1043-1045	3
β-strand	1050	1	10
α-helix	1051-1052	2
α-helix	1058-1068	11
β-strand	1069	1	11
α-helix	1071-1079	9
β-strand	1089	1	12
β-strand	1092-1094	3	13
β-strand	1095	1	11
α-helix	1096	1
α-helix	1103-1113	11
α-helix	1121-1132	12
α-helix	1136-1147	12
α-helix	1164-1174	11
α-helix	1178-1180	3
α-helix	1193-1202	10
β-strand	1207-1211	5	14
β-strand	1231-1233	3	14
β-strand	1248-1252	5	14
β-strand	1257-1259	3	14
β-strand	1260-1262	3	13
β-strand	1263	1	10
β-strand	1270	1	12
β-strand	1272-1274	3	15
β-strand	1276-1278	3	16
β-strand	1283-1285	3	16
α-helix	1286-1287	2
β-strand	1288	1	14
α-helix	1293-1297	5
α-helix	1299-1306	8
β-strand	1309-1315	7	15
β-strand	1322-1329	8	15
α-helix	1330-1331	2
α-helix	1337-1339	3
α-helix	1341-1357	17
α-helix	1359-1361	3

Chain C: 21 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	2010-2014	5
α-helix	2015-2027	13
β-strand	2029-2030	2	17
α-helix	2037-2038	2
β-strand	2039-2040	2	17
α-helix	2043-2045	3
β-strand	2050	1	18
α-helix	2051-2052	2
α-helix	2058-2068	11
β-strand	2069	1	19
α-helix	2071-2079	9
β-strand	2089	1	20
β-strand	2092-2094	3	21
β-strand	2095	1	19
α-helix	2096	1
α-helix	2103-2113	11
α-helix	2121-2132	12
α-helix	2136-2147	12
α-helix	2164-2174	11
α-helix	2178-2180	3
α-helix	2193-2203	11
β-strand	2207-2211	5	22
β-strand	2231-2233	3	22
β-strand	2248-2252	5	22
β-strand	2257-2259	3	22
β-strand	2260-2262	3	21
β-strand	2263	1	18
β-strand	2270	1	20
β-strand	2272-2274	3	23
β-strand	2276-2278	3	24
β-strand	2283-2285	3	24
α-helix	2286-2287	2
β-strand	2288	1	22
α-helix	2293-2297	5
α-helix	2299-2306	8
β-strand	2309-2315	7	23
β-strand	2322-2329	8	23
α-helix	2330-2331	2
α-helix	2337-2339	3
α-helix	2341-2357	17
α-helix	2359-2361	3

Chain D: 21 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	3010-3014	5
α-helix	3015-3027	13
β-strand	3029-3030	2	25
α-helix	3037-3038	2
β-strand	3039-3040	2	25
α-helix	3043-3045	3
β-strand	3050	1	26
α-helix	3051-3052	2
α-helix	3058-3068	11
β-strand	3069	1	27
α-helix	3071-3079	9
β-strand	3089	1	28
β-strand	3092-3094	3	29
β-strand	3095	1	27
α-helix	3096	1
α-helix	3103-3113	11
α-helix	3121-3132	12
α-helix	3136-3147	12
α-helix	3164-3174	11
α-helix	3178-3180	3
α-helix	3193-3202	10
β-strand	3207-3211	5	30
β-strand	3231-3233	3	30
β-strand	3248-3252	5	30
β-strand	3257-3259	3	30
β-strand	3260-3262	3	29
β-strand	3263	1	26
β-strand	3270	1	28
β-strand	3272-3274	3	31
β-strand	3276-3278	3	32
β-strand	3283-3285	3	32
α-helix	3286-3287	2
β-strand	3288	1	30
α-helix	3293-3297	5
α-helix	3299-3306	8
β-strand	3309-3315	7	31
β-strand	3322-3329	8	31
α-helix	3330-3331	2
α-helix	3337-3339	3
α-helix	3341-3357	17
α-helix	3359-3361	3

Chain E: 21 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	4010-4014	5
α-helix	4015-4027	13
β-strand	4029-4030	2	33
α-helix	4037-4038	2
β-strand	4039-4040	2	33
α-helix	4043-4045	3
β-strand	4050	1	34
α-helix	4051-4052	2
α-helix	4058-4068	11
β-strand	4069	1	35
α-helix	4071-4079	9
β-strand	4089	1	36
β-strand	4092-4094	3	37
β-strand	4095	1	35
α-helix	4096	1
α-helix	4103-4113	11
α-helix	4121-4132	12
α-helix	4136-4147	12
α-helix	4167-4174	8
α-helix	4178-4180	3
α-helix	4193-4203	11
β-strand	4207-4211	5	38
β-strand	4231-4233	3	38
β-strand	4248-4252	5	38
β-strand	4257-4259	3	38
β-strand	4260-4262	3	37
β-strand	4263	1	34
β-strand	4270	1	36
β-strand	4272-4274	3	39
β-strand	4276-4278	3	40
β-strand	4283-4285	3	40
α-helix	4286-4287	2
β-strand	4288	1	38
α-helix	4293-4297	5
α-helix	4299-4306	8
β-strand	4309-4315	7	39
β-strand	4322-4329	8	39
α-helix	4330-4331	2
α-helix	4337-4339	3
α-helix	4341-4357	17
α-helix	4359-4361	3

Chain F: 21 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	5010-5014	5
α-helix	5015-5027	13
β-strand	5029-5030	2	41
α-helix	5037-5038	2
β-strand	5039-5040	2	41
α-helix	5043-5045	3
β-strand	5050	1	42
α-helix	5051-5052	2
α-helix	5058-5068	11
β-strand	5069	1	43
α-helix	5071-5079	9
β-strand	5089	1	44
β-strand	5092-5094	3	45
β-strand	5095	1	43
α-helix	5096	1
α-helix	5103-5113	11
α-helix	5121-5132	12
α-helix	5136-5147	12
α-helix	5167-5174	8
α-helix	5178-5180	3
α-helix	5193-5203	11
β-strand	5207-5211	5	46
β-strand	5231-5233	3	46
β-strand	5248-5252	5	46
β-strand	5257-5259	3	46
β-strand	5260-5262	3	45
β-strand	5263	1	42
β-strand	5270	1	44
β-strand	5272-5274	3	47
β-strand	5276-5278	3	48
β-strand	5283-5285	3	48
α-helix	5286-5287	2
β-strand	5288	1	46
α-helix	5293-5297	5
α-helix	5299-5306	8
β-strand	5309-5315	7	47
β-strand	5322-5329	8	47
α-helix	5330-5331	2
α-helix	5337-5339	3
α-helix	5341-5357	17
α-helix	5359-5361	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tumor necrosis factor, alpha-induced protein 3	A, B, C, D, E, F	protein	390	Homo sapiens	P21580 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F), FASTA

>3DKB_1 Tumor necrosis factor, alpha-induced protein 3 (chains A, B, C, D, E, F)
MGSSHHHHHHSSGLVPRGSHMAEQVLPQALYLSNMRKAVKIRERTPEDIFKPTNGIIHHF
KTMHRYTLEMFRTCQFCPQFREIIHKALIDRNIQATLESQKKLNWCREVRKLVALKTNGD
GNCLMHATSQYMWGVQDTDLVLRKALFSTLKETDTRNFKFRWQLESLKSQEFVETGLCYD
TRNWNDEWDNLIKMASTDTPMARSGLQYNSLEEIHIFVLCNILRRPIIVISDKMLRSLES
GSNFAPLKVGGIYLPLHWPAQECYRYPIVLGYDSHHFVPLVTLKDSGPEIRAVPLVNRDR
GRFEDLKVHFLTDPENEMKEKLLKEYLMVIEIPVQGWDHGTTHLINAAKLDEANLPKEIN
LVDDYFELVQHEYKKWQENSEQGRREGHAQ

Primary citation

Molecular basis for the unique deubiquitinating activity of the NF-kappaB inhibitor A20. Lin, S.-C., Chung, J.Y., Lamothe, B. et al. J Mol Biol (2008) 376:526-540. DOI 10.1016/j.jmb.2007.11.092 · PubMed

Other PDB entries of the same protein (UniProt P21580 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3VUX 1.7 Å, Crystal structure of A20 ZF7 in complex with linear ubiquitin, form II
3ZJE 1.84 Å, A20 OTU domain in reversibly oxidised (SOH) state
3ZJD 1.87 Å, A20 OTU domain in reduced, active state at 1.87 A resolution
3ZJG 1.92 Å, A20 OTU domain with irreversibly oxidised Cys103 from 60 min H2O2 soak.
3VUW 1.95 Å, Crystal structure of A20 ZF7 in complex with linear ubiquitin, form I
3VUY 1.98 Å, Crystal structure of A20 ZF7 in complex with linear tetraubiquitin
3ZJF 2.2 Å, A20 OTU domain with irreversibly oxidised Cys103 from 270 min H2O2 soak.
3OJ3 2.5 Å, Crystal structure of the A20 ZnF4 and ubiquitin complex
5V3P 2.5 Å, Human A20 OTU domain (I325N) with acetamidylated C103
5LRX 2.85 Å, Structure of A20 OTU domain bound to ubiquitin
5V3B 3.0 Å, Human A20 OTU domain (WT) with acetamidylated C103
2VFJ 3.2 Å, Structure of the A20 Ovarian Tumour (OTU) domain

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