7KPB: Human TNF-alpha TNFR1 complex

Human TNF-alpha TNFR1 complex bound to conformationally selective antibody. Determined by X-ray diffraction at 3.0 Å resolution. Released 13 Jan 2021.

Method: X-ray diffraction
Resolution: 3.0 Å
Organisms: Homo sapiens, Mus musculus
Chains: 7
Atoms: 8,525
Mol. weight: 134.09 kDa
Ligands: NAG, D84
Released: 13 Jan 2021

Explore 7KPB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7KPB contains 34 α-helices and 121 β-strands across 7 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: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
β-strand	13-18	6	1
β-strand	28-29	2	1
β-strand	32	1	2
β-strand	36-38	3	1
β-strand	42-44	3	3
β-strand	47-49	3	3
β-strand	54-67	14	1
α-helix	73-74	2
β-strand	76-83	8	3
β-strand	90-98	9	3
α-helix	104-106	3
β-strand	113-126	14	1
β-strand	131-136	6	3
α-helix	139-141	3
β-strand	142	1	1
β-strand	150-156	7	1

Chain B: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
β-strand	13-18	6	4
β-strand	28-29	2	4
β-strand	36-38	3	4
β-strand	42-44	3	5
β-strand	47-49	3	5
β-strand	54-67	14	4
β-strand	76-83	8	5
β-strand	91-98	8	5
β-strand	113-126	14	4
β-strand	131-136	6	5
α-helix	139-141	3
β-strand	142	1	4
β-strand	151-156	6	4

Chain C: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	6
β-strand	28-29	2	6
β-strand	37-38	2	6
β-strand	42-44	3	7
β-strand	47-49	3	7
β-strand	54-65	12	6
β-strand	76-83	8	7
β-strand	91-98	8	7
β-strand	115-126	12	6
β-strand	131-136	6	7
α-helix	139-141	3
β-strand	142	1	6
β-strand	151-156	6	6

Chain E: 7 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	19-21	3	17
β-strand	29-31	3	17
α-helix	32	1
β-strand	33	1	18
α-helix	34	1
β-strand	37-41	5	19
β-strand	51-54	4	19
β-strand	59-60	2	20
β-strand	65	1	18
β-strand	70	1	2
β-strand	71-72	2	20
α-helix	73-74	2
α-helix	78-80	3
β-strand	83-86	4	21
α-helix	87-88	2
β-strand	89	1	22
β-strand	92	1	22
β-strand	95-97	3	21
β-strand	102-106	5	23
β-strand	112-116	5	23
α-helix	117-118	2
β-strand	123-127	5	24
α-helix	134-135	2
β-strand	136-139	4	24
β-strand	144-146	3	25
β-strand	149-151	3	25

Chain F: 7 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	19-21	3	8
β-strand	29-31	3	8
α-helix	32	1
β-strand	33	1	9
α-helix	34	1
β-strand	37-41	5	10
β-strand	51-54	4	10
α-helix	55-56	2
β-strand	59-60	2	11
β-strand	65	1	9
β-strand	71-72	2	11
α-helix	73-74	2
α-helix	78-80	3
β-strand	83-86	4	12
β-strand	89	1	13
β-strand	92	1	13
β-strand	95-97	3	12
β-strand	102-106	5	14
β-strand	112-116	5	14
α-helix	117-118	2
β-strand	123-127	5	15
β-strand	136-139	4	15
α-helix	140	1
β-strand	143-145	3	16
β-strand	150-152	3	16

Chain H: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	31
β-strand	11-12	2	32
β-strand	18-25	8	31
α-helix	29-31	3
β-strand	33-39	7	33
β-strand	45-51	7	33
β-strand	58-60	3	33
α-helix	62-64	3
β-strand	68-73	6	31
β-strand	78-83	6	31
α-helix	88-90	3
β-strand	92-101	10	33
β-strand	106-111	6	33
β-strand	115-117	3	33
β-strand	118-119	2	32
α-helix	122-124	3
β-strand	125	1	34
β-strand	128-130	3	35
β-strand	143-146	4	36
β-strand	149-153	5	35
β-strand	154	1	34
β-strand	161-162	2	37
α-helix	163-165	3
β-strand	171	1	36
α-helix	174-176	3
β-strand	177-178	2	35
β-strand	183-186	4	35
β-strand	189-192	4	36
β-strand	202-207	6	37
β-strand	212-217	6	37

Chain L: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	26
β-strand	10-13	4	27
β-strand	19-25	7	26
β-strand	33-38	6	27
β-strand	45-49	5	27
β-strand	53-54	2	27
α-helix	55	1
β-strand	62-66	5	26
β-strand	70-75	6	26
α-helix	80-82	3
β-strand	85-90	6	27
β-strand	93	1	3
α-helix	96	1
β-strand	98	1	27
β-strand	102-106	5	27
β-strand	111	1	28
β-strand	114-118	5	29
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	29
β-strand	140	1	28
β-strand	145-150	6	30
β-strand	153-155	3	30
β-strand	159	1	29
β-strand	162-163	2	29
α-helix	165-167	3
β-strand	173-182	10	29
α-helix	183-186	4
β-strand	191-198	8	30
β-strand	201-210	10	30

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tumor necrosis factor	A, B, C	protein	158	Homo sapiens	P01375 (AlphaFold model)
Tumor necrosis factor receptor superfamily member 1A	E, F	protein	144	Homo sapiens	P19438 (AlphaFold model)
Fab1974 - Light Chain	L	protein	214	Mus musculus
Fab1974 - Heavy Chain	H	protein	223	Mus musculus

Sequence of entity 1 (A, B, C), FASTA

>7KPB_1 Tumor necrosis factor (chains A, B, C)
SVRSSSRTPSDKPVAHVVANPQAEGQLQWLNRRANALLANGVELRDNQLVVPSEGLYLIY
SQVLFKGQGCPSTHVLLTHTISRIAVSYQTKVNLLSAIKSPCQRETPEGAEAKPWYEPIY
LGGVFQLEKGDRLSAEINRPDYLDFAESGQVYFGIIAL

Sequence of entity 2 (E, F), FASTA

>7KPB_2 Tumor necrosis factor receptor superfamily member 1A (chains E, F)
GSVCPQGKYIHPQDNSICCTKCHKGTYLYNDCPGPGQDTDCRECESGSFTASENHLRHCL
SCSKCRKEMGQVEISSCTVDRDTVCGCRKNQYRHYWSENLFQCFNCSLCLNGTVHLSCQE
KQNTVCTCHAGFFLRENECVSSSN

Sequence of entity 3 (L), FASTA

>7KPB_3 Fab1974 - Light Chain (chains L)
DIQMTQSPASLPASPEEIVTITCQASQDIGNWLSWYQQKPGKSPQLLIYGATSLADGVPS
RFSASRSGTQYSLKISRLQVEDFGIFYCLQGQSTPYTFGAGTKLELKRTDAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 4 (H), FASTA

>7KPB_4 Fab1974 - Heavy Chain (chains H)
DVQLVESGGGLVQPGRSLKLSCAASGFTFSAYYMAWVRQAPTKGLEWVASINYDGANTFY
RDSVKGRFTVSRDNARSSLYLQMDSLRSEDTATYYCTTEAYGYNSNWFGYWGQGTLVTVS
SAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQS
DLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
D84	5-(1-{[2-(difluoromethoxy)phenyl]methyl}-2-{[3-(2-oxopyrrolidin-1-yl)phenoxy]me…	C31 H26 F2 N4 O4	1

Water and common crystallization additives (GOL) are not listed.

Primary citation

A conformation-selective monoclonal antibody against a small molecule-stabilised signalling-deficient form of TNF. Lightwood, D.J., Munro, R.J., Porter, J. et al. Nat Commun (2021) 12:583-583. DOI 10.1038/s41467-020-20825-6 · 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 structure collections

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