3NFP: Fab fragment of therapeutic antibody daclizumab

Crystal structure of the Fab fragment of therapeutic antibody daclizumab in complex with IL-2Ra (CD25) ectodomain. Determined by X-ray diffraction at 2.86 Å resolution. Released 15 Sept 2010.

Method: X-ray diffraction
Resolution: 2.86 Å
Organism: Homo sapiens
Chains: 6
Atoms: 8,421
Mol. weight: 143.12 kDa
Released: 15 Sept 2010

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

Secondary structure: helices and β-sheets

3NFP contains 34 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: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
α-helix	7-9	3
β-strand	10-12	3	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-39	6	2
β-strand	45-51	7	2
β-strand	58-60	3	2
β-strand	68-73	6	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-98	7	2
β-strand	101	1	3
β-strand	106	1	2
β-strand	110-114	5	2
β-strand	120	1	4
β-strand	123-127	5	5
β-strand	138-148	11	5
β-strand	149	1	4
β-strand	154	1	6
β-strand	157	1	6
β-strand	166-168	3	5
α-helix	169-171	3
β-strand	172-173	2	5
β-strand	179-188	10	5
α-helix	189-191	3
β-strand	197-203	7	6
α-helix	204-206	3
β-strand	208-214	7	6

Chain B: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	7
β-strand	10-13	4	2
β-strand	19-29	11	7
β-strand	33-37	5	2
β-strand	44-48	5	2
β-strand	52-53	2	2
α-helix	54	1
β-strand	61-74	14	7
α-helix	79-81	3
β-strand	84-89	6	2
α-helix	95	1
β-strand	96-97	2	2
β-strand	101-105	5	2
α-helix	106	1
β-strand	110	1	8
α-helix	111-112	2
β-strand	113-117	5	9
α-helix	118-120	3
α-helix	121-124	4
β-strand	128-138	11	9
β-strand	139	1	8
β-strand	144-149	6	10
β-strand	158-162	5	9
β-strand	172-181	10	9
α-helix	182-185	4
β-strand	190-196	7	10
β-strand	204-209	6	10

Chain H: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	11
α-helix	7-9	3
β-strand	10-12	3	12
β-strand	18-25	8	11
β-strand	34-39	6	12
β-strand	45-51	7	12
β-strand	58-60	3	12
α-helix	62-64	3
β-strand	68-73	6	11
β-strand	78-83	6	11
α-helix	88-90	3
β-strand	92-98	7	12
β-strand	101	1	13
β-strand	106	1	12
β-strand	110-114	5	12
β-strand	120	1	14
β-strand	123-127	5	15
β-strand	133	1	16
β-strand	135	1	16
β-strand	138-148	11	15
β-strand	149	1	14
β-strand	154-157	4	17
β-strand	166-168	3	15
α-helix	169-171	3
β-strand	172-173	2	15
β-strand	179-188	10	15
α-helix	191-194	4
β-strand	198-203	6	17
α-helix	204-206	3
β-strand	208-213	6	17

Chain I: 2 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	23
α-helix	7-10	4
β-strand	13-16	4	24
β-strand	20-21	2	25
β-strand	25-27	3	26
β-strand	30	1	27
β-strand	43-45	3	26
β-strand	46-48	3	28
β-strand	53-55	3	28
β-strand	103-104	2	25
α-helix	106-109	4
β-strand	113	1	27
β-strand	120	1	26
β-strand	122	1	23
β-strand	126-131	6	24
β-strand	137	1	29
β-strand	144-146	3	24
β-strand	147-149	3	30
β-strand	153	1	13
β-strand	154-156	3	30
β-strand	163	1	29

Chain K: 2 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
β-strand	16	1	31
β-strand	20-21	2	32
β-strand	25-26	2	33
β-strand	37	1	34
β-strand	44-45	2	33
β-strand	46-48	3	35
β-strand	53-55	3	35
β-strand	61	1	34
β-strand	103-104	2	32
α-helix	105-109	5
β-strand	119-120	2	33
β-strand	126-128	3	31
β-strand	144-146	3	31
β-strand	147-149	3	36
β-strand	153	1	3
β-strand	154-156	3	36

Chain L: 10 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	18
β-strand	10-13	4	19
β-strand	19-29	11	18
β-strand	33-37	5	19
α-helix	42-43	2
β-strand	44-48	5	19
β-strand	52-53	2	19
α-helix	54	1
β-strand	61-74	14	18
α-helix	79-81	3
β-strand	84-89	6	19
α-helix	95	1
β-strand	96-97	2	19
β-strand	101-105	5	19
α-helix	106	1
β-strand	110	1	20
α-helix	111-112	2
β-strand	113-117	5	21
α-helix	118-120	3
α-helix	121-124	4
β-strand	128-138	11	21
β-strand	139	1	20
β-strand	144-149	6	22
β-strand	153	1	22
β-strand	158-162	5	21
α-helix	163-166	4
β-strand	172-181	10	21
α-helix	182-185	4
β-strand	190-196	7	22
β-strand	204-209	6	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Heavy chain of Fab fragment of daclizumab	A, H	protein	216	Homo sapiens
Light chain of Fab fragment of daclizumab	B, L	protein	212	Homo sapiens
Interleukin-2 receptor subunit alpha	I, K	protein	223	Homo sapiens	P01589 (AlphaFold model)

Sequence of entity 1 (A, H), FASTA

>3NFP_1 Heavy chain of Fab fragment of daclizumab (chains A, H)
QVQLVQSGAEVKKPGSSVKVSCKASGYTFTSYRMHWVRQAPGQGLEWIGYINPSTGYTEY
NQKFKDKATITADESTNTAYMELSSLRSEDTAVYYCARGGGVFDYWGQGTLVTVSSASTK
GPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYS
LSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP

Sequence of entity 2 (B, L), FASTA

>3NFP_2 Light chain of Fab fragment of daclizumab (chains B, L)
DIQMTQSPSTLSASVGDRVTITCSASSSISYMHWYQQKPGKAPKLLIYTTSNLASGVPAR
FSGSGSGTEFTLTISSLQPDDFATYYCHQRSTYPLTFGQGTKVEVKRTVAAPSVFIFPPS
DEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTL
SKADYEKHKVYACEVTHQGLSSPVTKSFNRGE

Sequence of entity 3 (I, K), FASTA

>3NFP_3 Interleukin-2 receptor subunit alpha (chains I, K)
ELCDDDPPEIPHATFKAMAYKEGTMLNCECKRGFRRIKSGSLYMLCTGNSSHSSWDNQCQ
CTSSATRNTTKQVTPQPEEQKERKTTEMQSPMQPVDQASLPGHCREPPPWENEATERIYH
FVVGQMVYYQCVQGYRALHRGPAESVCKMTHGKTRWTQPQLICTGEMETSQFPGEEKPQA
SPEGRPESETSCLVTTTDFQIQTEMAATMETSIFTTEHHHHHH

Primary citation

Structural basis of immunosuppression by the therapeutic antibody daclizumab. Yang, H., Wang, J., Du, J. et al. Cell Res (2010) 20:1361-1371. DOI 10.1038/cr.2010.130 · PubMed

Other PDB entries of the same protein (UniProt P01589 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6YIO 1.83 Å, Crystal structure of FAB RG6292 in complex with CD25 ecd
2B5I 2.3 Å, cytokine receptor complex
1Z92 2.8 Å, structure of interleukin-2 with its alpha receptor
3IU3 2.9 Å, Crystal structure of the Fab fragment of therapeutic antibody Basiliximab in complex…
9KMC 2.97 Å, Cryo-EM structure of the heterotrimeric interleukin-2 receptor in complex with…
2ERJ 3.0 Å, Crystal structure of the heterotrimeric interleukin-2 receptor in complex with…
7F9W 3.2 Å, CD25 in complex with Fab
7ZMZ 3.2 Å, Engineered Interleukin 2 bound to CD25 receptor
6VWU 3.4 Å, X-ray structure of ALKS 4230, a fusion of circularly permuted human Interleukin-2 and…

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