3ALQ: TNF-TNFR2 complex

Crystal structure of TNF-TNFR2 complex. Determined by X-ray diffraction at 3.0 Å resolution. Released 17 Nov 2010.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 12
Atoms: 13,927
Mol. weight: 216.74 kDa
Ligands: CO
Released: 17 Nov 2010

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

Secondary structure: helices and β-sheets

3ALQ contains 55 α-helices and 188 β-strands across 12 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.

Chains A, B and C: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	1
β-strand	28-29	2	1
β-strand	36-38	3	1
β-strand	42-44	3	2
β-strand	47-49	3	2
β-strand	54-66	13	1
β-strand	76-84	9	2
β-strand	87-98	12	2
β-strand	114-126	13	1
β-strand	131-136	6	2
α-helix	139-141	3
β-strand	142	1	1
β-strand	151-156	6	1

Chains D and E: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	7
β-strand	28-29	2	7
β-strand	36-38	3	7
β-strand	42-44	3	8
β-strand	47-49	3	8
β-strand	54-66	13	7
β-strand	76-83	8	8
β-strand	91-98	8	8
β-strand	114-126	13	7
β-strand	131-136	6	8
α-helix	139-141	3
β-strand	142	1	7
β-strand	151-156	6	7

Chain F: 0 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	11
β-strand	28-29	2	11
β-strand	36-38	3	11
β-strand	42-44	3	12
β-strand	47-49	3	12
β-strand	54-66	13	11
β-strand	76-83	8	12
β-strand	91-98	8	12
β-strand	114-126	13	11
β-strand	131-136	6	12
β-strand	142	1	11
β-strand	151-156	6	11

Chain R: 8 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	22-25	4	13
β-strand	30-33	4	13
α-helix	34	1
β-strand	35	1	14
α-helix	36	1
β-strand	39-43	5	15
β-strand	52-55	4	15
β-strand	60-61	2	16
β-strand	66	1	14
α-helix	71	1
β-strand	72-73	2	16
α-helix	74	1
β-strand	82-86	5	17
β-strand	95-98	4	17
α-helix	99	1
β-strand	102-107	6	18
β-strand	112-117	6	18
α-helix	118-119	2
β-strand	121	1	19
β-strand	125-129	5	20
β-strand	138-141	4	20
α-helix	142-143	2
β-strand	146-147	2	21
β-strand	152	1	19
β-strand	158-159	2	21
α-helix	160	1

Chain S: 8 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	22-25	4	22
β-strand	30-33	4	22
α-helix	34	1
β-strand	35	1	23
α-helix	36	1
β-strand	39-43	5	24
β-strand	52-55	4	24
β-strand	60-61	2	25
β-strand	66	1	23
α-helix	71	1
β-strand	72-73	2	25
α-helix	74-78	5
β-strand	82-86	5	26
β-strand	95-98	4	26
α-helix	99	1
β-strand	102-107	6	27
β-strand	112-117	6	27
α-helix	118-119	2
β-strand	121	1	28
β-strand	125-129	5	29
β-strand	138-141	4	29
β-strand	146-147	2	30
β-strand	152	1	28
α-helix	155-157	3
β-strand	158-159	2	30
α-helix	160-161	2

Chain T: 7 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	22-25	4	31
β-strand	30-33	4	31
α-helix	34	1
β-strand	35	1	32
α-helix	36	1
β-strand	39-43	5	33
β-strand	52-55	4	33
β-strand	60-61	2	34
β-strand	66	1	32
α-helix	71	1
β-strand	72-73	2	34
α-helix	74-78	5
β-strand	82-86	5	35
β-strand	95-98	4	35
α-helix	99	1
β-strand	102-108	7	36
β-strand	111-117	7	36
α-helix	118-119	2
β-strand	121	1	37
β-strand	125-129	5	38
β-strand	138-141	4	38
β-strand	146-147	2	39
β-strand	152	1	37
β-strand	158-159	2	39
α-helix	160-162	3
β-strand	168	1	40
β-strand	177	1	40

Chain U: 8 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	22-25	4	41
β-strand	30-33	4	41
β-strand	35	1	42
α-helix	36	1
β-strand	39-43	5	43
β-strand	52-55	4	43
β-strand	60-61	2	44
β-strand	66	1	42
α-helix	71	1
β-strand	72-73	2	44
α-helix	74-78	5
β-strand	82-86	5	45
β-strand	95-98	4	45
α-helix	99	1
β-strand	102-107	6	46
β-strand	112-117	6	46
α-helix	118-119	2
β-strand	121	1	47
β-strand	125-129	5	48
α-helix	137	1
β-strand	138-141	4	48
α-helix	142-143	2
β-strand	146-147	2	49
β-strand	152	1	47
β-strand	158-159	2	49
α-helix	160-162	3
β-strand	168	1	50
β-strand	177	1	50

Chain V: 10 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	22-25	4	51
β-strand	30-33	4	51
α-helix	34	1
β-strand	35	1	52
α-helix	36	1
β-strand	39-43	5	53
α-helix	50-51	2
β-strand	52-55	4	53
β-strand	60-61	2	54
β-strand	66	1	52
α-helix	71	1
β-strand	72-73	2	54
α-helix	74-78	5
β-strand	82-86	5	55
β-strand	95-98	4	55
α-helix	99	1
β-strand	102-107	6	56
β-strand	112-117	6	56
α-helix	118-119	2
β-strand	121	1	57
α-helix	122	1
β-strand	125-129	5	58
β-strand	138-141	4	58
α-helix	142-143	2
β-strand	146-147	2	59
β-strand	152	1	57
β-strand	158-159	2	59
α-helix	160	1
β-strand	168	1	60
β-strand	177	1	60

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tumor necrosis factor	A, B, C, D, E, F	protein	157	Homo sapiens	P01375 (AlphaFold model)
Tumor necrosis factor receptor superfamily member 1B	R, S, T, U, V, W	protein	173	Homo sapiens	P20333 (AlphaFold model)

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

>3ALQ_1 Tumor necrosis factor (chains A, B, C, D, E, F)
VRSSSRTPSDMPVAHVVANPQAEGQLQWLNRRANALLANGVELRDNQLVVPSEGLYLIYS
QVLFSGQGCPSTHVLLTHTISRIAVSYQTPVNLLSAIRSPCQRETPEGAEANPWYEPIYL
GGVFQLEPGDRLSAEINRPDYLDFAESGQVYFGIIAL

Sequence of entity 2 (R, S, T, U, V, W), FASTA

>3ALQ_2 Tumor necrosis factor receptor superfamily member 1B (chains R, S, T, U, V, W)
APEPGSTCRLREYYDQTAQMCCSKCSPGQHAKVFCTKTSDTVCDSCEDSTYTQLWNWVPE
CLSCGSRCSSDQVETQACTREQNRICTCRPGWYCALSKQEGCRLCAPLRKCRPGFGVARP
GTETSDVVCKPCAPGTFSNTTSSTDICRPHQICNVVAIPGNASMDAVCTSTSP

Ligands and cofactors

ID	Name	Formula	Copies
CO	Cobalt (II) ion	Co	6

Primary citation

Solution of the Structure of the TNF-TNFR2 Complex. Mukai, Y., Nakamura, T., Yoshikawa, M. et al. Sci Signal (2010) 3:ra83-ra83. DOI 10.1126/scisignal.2000954 · PubMed

Other PDB entries of the same protein (UniProt P01375 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9OJO 1.36 Å, Crystal structure of TNF alpha in complex with compound 1
5UUI 1.4 Å, Crystal Structure of Spin-Labeled T77C TNFa
4Y6O 1.6 Å, Human SIRT2 in complex with myristoylated peptide (TNF-alphaK20myr)
2E7A 1.8 Å, TNF Receptor Subtype One-selective TNF Mutant with Antagonistic Activity
4TSV 1.8 Å, High resolution crystal structure of a human tnf-alpha mutant
9OJS 1.85 Å, Crystal structure of TNF alpha in complex with compound 4
5M2J 1.9 Å, Complex between human TNF alpha and Llama VHH2
9BN7 1.92 Å, X-ray crystal structure of TNFa-VNAR C4 complex
2AZ5 2.1 Å, Crystal Structure of TNF-alpha with a small molecule inhibitor
3L9J 2.1 Å, Selection of a novel highly specific TNFalpha antagonist: Insight from the crystal…
7JRA 2.1 Å, HUMAN TNF-ALPHA IN COMPLEX WITH 2-[5-(3-chloro-4-{[(1R)-1-(2-fluorophenyl)ethyl]amino}qui…
5M2I 2.15 Å, Structure of human Tumor Necrosis Factor (TNF) in complex with the Llama VHH1

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