4G3Y: TNF-alpha

Crystal structure of TNF-alpha in complex with Infliximab Fab fragment. Determined by X-ray diffraction at 2.6 Å resolution. Released 27 Mar 2013.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 3
Atoms: 4,599
Mol. weight: 65.19 kDa
Released: 27 Mar 2013

Explore 4G3Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4G3Y contains 19 α-helices and 60 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 C: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	14
β-strand	28-29	2	14
β-strand	36-38	3	14
β-strand	42-44	3	15
β-strand	47-49	3	15
β-strand	54-67	14	14
β-strand	76-83	8	15
β-strand	90-98	9	15
α-helix	110-111	2
β-strand	113-126	14	14
β-strand	131-136	6	15
α-helix	139-141	3
β-strand	142	1	14
β-strand	151-155	5	14

Chain H: 8 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	10-12	3	8
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	33-40	8	8
β-strand	44-51	8	8
β-strand	55	1	9
β-strand	57	1	9
β-strand	60-62	3	8
β-strand	70-75	6	7
β-strand	80-85	6	7
α-helix	90-92	3
β-strand	94-101	8	8
β-strand	107-110	4	8
β-strand	114-118	5	8
α-helix	122-123	2
β-strand	124	1	10
β-strand	127-131	5	11
α-helix	132-134	3
β-strand	142-152	11	11
β-strand	153	1	10
β-strand	158-161	4	12
α-helix	162-164	3
β-strand	170-172	3	11
α-helix	173-175	3
β-strand	176-177	2	11
β-strand	183-192	10	11
α-helix	194-196	3
β-strand	201-202	2	13
β-strand	203-207	5	12
α-helix	208-210	3
β-strand	212-214	3	12
β-strand	217-218	2	13

Chain L: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	1
β-strand	10-13	4	2
β-strand	19-25	7	1
β-strand	33-38	6	2
β-strand	45-49	5	2
β-strand	53-54	2	2
α-helix	55	1
β-strand	62-67	6	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	84-90	7	2
α-helix	96	1
β-strand	97-98	2	2
β-strand	102-106	5	2
β-strand	111	1	3
α-helix	112-113	2
β-strand	114-118	5	4
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	4
β-strand	140	1	3
β-strand	144-145	2	5
β-strand	148-150	3	6
β-strand	153-154	2	6
α-helix	155	1
β-strand	159-163	5	4
α-helix	164-167	4
β-strand	173-182	10	4
α-helix	183-186	4
β-strand	191-196	6	6
β-strand	197-198	2	5
β-strand	205-210	6	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
infliximab Fab L	L	protein	214	Homo sapiens
infliximab Fab H	H	protein	226	Homo sapiens
Tumor necrosis factor	C	protein	157	Homo sapiens	P01375 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>4G3Y_1 infliximab Fab L (chains L)
DILLTQSPAILSVSPGERVSFSCRASQFVGSSIHWYQQRTNGSPRLLIKYASESMSGIPS
RFSGSGSGTDFTLSINTVESEDIADYYCQQSHSWPFTFGSGTNLEVKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (H), FASTA

>4G3Y_2 infliximab Fab H (chains H)
EVKLEESGGGLVQPGGSMKLSCVASGFIFSNHWMNWVRQSPEKGLEWVAEIRSKSINSAT
HYAESVKGRFTISRDDSKSAVYLQMTDLRTEDTGVYYCSRNYYGSTYDYWGQGTTLTVSS
ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKT

Sequence of entity 3 (C), FASTA

>4G3Y_3 Tumor necrosis factor (chains C)
VRSSSRTPSDKPVAHVVANPQAEGQLQWLNRRANALLANGVELRDNQLVVPSEGLYLIYS
QVLFKGQGCPSTHVLLTHTISRIAVSYQTKVNLLSAIKSPCQRETPEGAEAKPWYEPIYL
GGVFQLEKGDRLSAEINRPDYLDFAESGQVYFGIIAL

Primary citation

Structural basis for treating tumor necrosis factor alpha (TNFalpha)-associated diseases with the therapeutic antibody infliximab. Liang, S.Y., Dai, J.X., Hou, S. et al. J Biol Chem (2013) 288:13799-13807. DOI 10.1074/jbc.M112.433961 · 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

4G3Y is part of these collections:

Antibodies and the immune system

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