4YPG: Sifalimumab light chain

Structural Insights Into the Neutralization Properties of a Human Anti-Interferon Monoclonal Antibody. Determined by X-ray diffraction at 3.0 Å resolution. Released 6 May 2015.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 6
Atoms: 9,219
Mol. weight: 131.15 kDa
Ligands: NI
Released: 6 May 2015

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

Secondary structure: helices and β-sheets

4YPG contains 57 α-helices and 90 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: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	1
β-strand	10-13	4	2
β-strand	19-24	6	1
α-helix	31-33	3
β-strand	34-39	6	2
β-strand	47-49	3	2
α-helix	54	1
β-strand	55	1	2
α-helix	56	1
β-strand	63-68	6	1
β-strand	71-76	6	1
α-helix	81-83	3
β-strand	86-91	6	2
β-strand	98-99	2	2
β-strand	103-107	5	2
β-strand	112	1	3
α-helix	113-114	2
β-strand	115-119	5	4
α-helix	123-128	6
β-strand	130-140	11	4
β-strand	141	1	3
β-strand	145-151	7	5
β-strand	154-155	2	5
α-helix	156	1
β-strand	160-161	2	4
β-strand	164	1	4
α-helix	166-168	3
β-strand	174-183	10	4
α-helix	184-188	5
β-strand	192-199	8	5
β-strand	206-211	6	5

Chain B: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	6
β-strand	10-12	3	7
β-strand	18-25	8	6
α-helix	29-31	3
β-strand	34-39	6	7
β-strand	46-51	6	7
β-strand	58-60	3	7
α-helix	62-64	3
β-strand	65	1	6
β-strand	68-73	6	6
β-strand	78-83	6	6
α-helix	88-90	3
β-strand	92-98	7	7
α-helix	101-103	3
β-strand	106	1	7
β-strand	107	1	6
β-strand	110-114	5	7
β-strand	120	1	8
α-helix	121-122	2
β-strand	123-127	5	9
α-helix	131-133	3
β-strand	134	1	9
β-strand	138-148	11	9
β-strand	149	1	8
β-strand	154-157	4	10
β-strand	166-168	3	9
α-helix	169-171	3
β-strand	172-173	2	9
β-strand	179-188	10	9
α-helix	189-192	4
β-strand	198-203	6	10
α-helix	204-206	3
β-strand	208-213	6	10

Chain C: 9 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	4-7	4
β-strand	10	1	11
α-helix	11	1
α-helix	12-21	10
α-helix	40-42	3
α-helix	53-66	14
α-helix	70-75	6
α-helix	78-100	23
α-helix	113-132	20
α-helix	137-152	16
β-strand	155	1	11

Chain D: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	4-8	5
α-helix	10-11	2
α-helix	12-21	10
α-helix	26-28	3
α-helix	40-42	3
α-helix	52-66	15
α-helix	70-75	6
α-helix	78-100	23
α-helix	113-132	20
α-helix	137-154	18

Chain H: 11 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	12
α-helix	7-9	3
β-strand	10-12	3	13
β-strand	18-25	8	12
α-helix	29-31	3
β-strand	34-39	6	13
β-strand	45-51	7	13
β-strand	58-60	3	13
α-helix	62-64	3
β-strand	68-73	6	12
β-strand	78-83	6	12
α-helix	88-90	3
β-strand	92-98	7	13
α-helix	101-103	3
β-strand	106	1	13
β-strand	110-114	5	13
α-helix	117-119	3
β-strand	120	1	14
α-helix	121-122	2
β-strand	123-127	5	15
α-helix	131-133	3
β-strand	134-135	2	15
β-strand	138-148	11	15
β-strand	149	1	14
β-strand	154-157	4	16
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	189-192	4
β-strand	198-203	6	16
α-helix	204-206	3
β-strand	208-213	6	16

Chain L: 9 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	17
β-strand	10-13	4	18
α-helix	18	1
β-strand	19-25	7	17
α-helix	31-33	3
β-strand	34-39	6	18
β-strand	46-49	4	18
α-helix	50-52	3
α-helix	54-56	3
β-strand	63-68	6	17
β-strand	71-76	6	17
α-helix	81-83	3
β-strand	86-91	6	18
β-strand	98-99	2	18
β-strand	103-107	5	18
β-strand	112	1	19
α-helix	113-114	2
β-strand	115-119	5	20
α-helix	123-128	6
β-strand	130-140	11	20
β-strand	141	1	19
β-strand	145-151	7	21
β-strand	154-155	2	21
β-strand	160-164	5	20
α-helix	165-168	4
β-strand	174-183	10	20
α-helix	184-189	6
β-strand	192-199	8	21
β-strand	206-211	6	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sifalimumab light chain	A, L	protein	215	Homo sapiens	Q6PJF2 (AlphaFold model)
Sifalimumab heavy chain	B, H	protein	219	Homo sapiens
Interferon alpha-2	C, D	protein	161	Homo sapiens	P01563 (AlphaFold model)

Sequence of entity 1 (A, L), FASTA

>4YPG_1 Sifalimumab light chain (chains A, L)
EIVLTQSPGTLSLSPGERATLSCRASQSVSSTYLAWYQQKPGQAPRLLIYGASSRATGIP
DRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSPRTFGQGTKVEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (B, H), FASTA

>4YPG_2 Sifalimumab heavy chain (chains B, H)
QVQLVQSGAEVKKPGASVKVSCKASGYTFTSYSISWVRQAPGQGLEWMGWISVYNGNTNY
AQKFQGRVTMTTDTSTSTAYLELRSLRSDDTAVYYCARDPIAAGYWGQGTLVTVSSASTK
GPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYS
LSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Sequence of entity 3 (C, D), FASTA

>4YPG_3 Interferon alpha-2 (chains C, D)
TSCDLPQTHSLGSRRTLMLLAQMRKISLFSCLKDRHDFGFPQEEFGNQFQKAETIPVLHE
MIQQIFNLFSTKDSSAAWDETLLDKFYTELYQQLNDLEACVIQGVGVTETPLMKEDSILA
VRKYFQRITLYLKEKKYSPCAWEVVRAEIMRSFSLSTNLQE

Ligands and cofactors

ID	Name	Formula	Copies
NI	Nickel (II) ion	Ni	6

Primary citation

Structural Insights into the Neutralization Properties of the Fully Human, Anti-interferon Monoclonal Antibody Sifalimumab. Oganesyan, V., Peng, L., Woods, R.M. et al. J Biol Chem (2015) 290:14979-14985. DOI 10.1074/jbc.M115.652156 · PubMed

Other PDB entries of the same protein (UniProt Q6PJF2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3EO0 1.75 Å, Structure of the Transforming Growth Factor-Beta Neutralizing Antibody GC-1008
8QH0 1.87 Å, Crystal structure of the SARS-CoV-2 RBD with the antibody Cv2.3194
1DN0 2.28 Å, Structure of the FAB fragment from a human IgM cold agglutinin
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8QH1 2.65 Å, Crystal structure of the SARS-CoV-2 RBD from the Omicron BA4 variant with the antibody…
1U6A 2.81 Å, Crystal Structure of the Broadly Neutralizing Anti-HIV Fab F105
1QLR 2.83 Å, Crystal structure of the FAB fragment of a human monoclonal IgM cold agglutinin
3EO1 3.1 Å, Structure of the Fab Fragment of GC-1008 in Complex with Transforming Growth Factor-Beta 3
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6MYY 3.8 Å, Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer, 3 Fabs…
6UDK 3.9 Å, HIV-1 bNAb 1-55 in complex with modified BG505 SOSIP-based immunogen RC1 and 10-1074
6MZJ 4.8 Å, Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer, 2 Fabs…

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