3WD5: TNFalpha

Crystal structure of TNFalpha in complex with Adalimumab Fab fragment. Determined by X-ray diffraction at 3.1 Å resolution. Released 14 Aug 2013.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 3
Atoms: 4,466
Mol. weight: 63.94 kDa
Released: 14 Aug 2013

Explore 3WD5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3WD5 contains 15 α-helices and 57 β-strands across 3 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: 2 helices, 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	42-43	2	2
β-strand	48-49	2	2
β-strand	54-67	14	1
β-strand	76-83	8	2
β-strand	90-98	9	2
β-strand	113-126	14	1
β-strand	131-136	6	2
α-helix	139-141	3
β-strand	142	1	1
α-helix	147-149	3
β-strand	151-156	6	1

Chain H: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	8
β-strand	10-12	3	9
β-strand	18-25	8	8
α-helix	29-31	3
β-strand	34-39	6	9
β-strand	45-51	7	9
β-strand	58-60	3	9
β-strand	68-73	6	8
β-strand	78-83	6	8
α-helix	88-90	3
β-strand	92-99	8	9
β-strand	108-111	4	9
β-strand	116-119	4	9
β-strand	125	1	10
α-helix	126-127	2
β-strand	128-132	5	11
α-helix	133-135	3
β-strand	143-153	11	11
β-strand	154	1	10
β-strand	159-162	4	12
α-helix	163-165	3
β-strand	171-173	3	11
α-helix	174-176	3
β-strand	177-178	2	11
β-strand	184-193	10	11
β-strand	203	1	13
β-strand	204-208	5	12
β-strand	213-215	3	12
β-strand	218	1	13

Chain L: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	3
β-strand	10-13	4	4
β-strand	19-25	7	3
β-strand	33-38	6	4
α-helix	43-44	2
β-strand	45-49	5	4
β-strand	53-54	2	4
α-helix	55	1
β-strand	62-63	2	3
β-strand	70-75	6	3
α-helix	80-82	3
β-strand	85-90	6	4
β-strand	98	1	4
β-strand	102-106	5	4
β-strand	111	1	5
α-helix	112-113	2
β-strand	114-118	5	6
α-helix	122-127	6
β-strand	129-139	11	6
β-strand	140	1	5
β-strand	145-150	6	7
β-strand	153-154	2	7
β-strand	159	1	6
β-strand	163	1	6
α-helix	164-167	4
β-strand	173-182	10	6
α-helix	183-186	4
β-strand	191-197	7	7
β-strand	205-210	6	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tumor necrosis factor	A	protein	157	Homo sapiens	P01375 (AlphaFold model)
Adalimumab Light Chain	L	protein	213	Homo sapiens
Adalimumab Heavy Chain	H	protein	219	Homo sapiens

Sequence of entity 1 (A), FASTA

>3WD5_1 Tumor necrosis factor (chains A)
VRSSSRTPSDKPVAHVVANPQAEGQLQWLNDRANALLANGVELRDNQLVVPSEGLYLIYS
QVLFKGQGCPSTHVLLTHTISRIAVSYQTKVNLLSAIKSPCQRETPEGAEAKPWYEPIYL
GGVFQLEKGDRLSAEINRPDYLDFAESGQVYFGIIAL

Sequence of entity 2 (L), FASTA

>3WD5_2 Adalimumab Light Chain (chains L)
DIQMTQSPSSLSASVGDRVTITCRASQGIRNYLAWYQQKPGKAPKLLIYAASTLQSGVPS
RFSGSGSGTDFTLTISSLQPEDVATYYCQRYNRAPYTFGQGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE

Sequence of entity 3 (H), FASTA

>3WD5_3 Adalimumab Heavy Chain (chains H)
EVQLVESGGGLVQPGRSLRLSCAASGFTFDDYAMHWVRQAPGKGLEWVSAITWNSGHIDY
ADSVEGRFTISRDNAKNSLYLDMNSLRAEDTAVYYCAKVSYLSTASSLDYWGQGTLVTVS
SASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQS
SGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKI

Primary citation

Comparison of the inhibition mechanisms of adalimumab and infliximab in treating tumor necrosis factor alpha-associated diseases from a molecular view. Hu, S., Liang, S.Y., Guo, H. et al. J Biol Chem (2013) 288:27059-27067. DOI 10.1074/jbc.M113.491530 · 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

Browse more

3WD5 is part of these collections:

Antibodies and the immune system

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