8SVE: Fab Heavy chain

Structure of Monomeric Interleukin-10 Grafted into and Antibody CDR. Determined by X-ray diffraction at 2.4 Å resolution. Released 22 May 2024.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 4
Atoms: 9,252
Mol. weight: 133.41 kDa
Released: 22 May 2024

Explore 8SVE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8SVE contains 53 α-helices and 89 β-strands across 4 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 H: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	2
β-strand	18-25	8	1
β-strand	34-41	8	3
β-strand	48-54	7	3
β-strand	59-61	3	3
α-helix	63-65	3
β-strand	69-74	6	1
β-strand	79-84	6	1
α-helix	89-91	3
β-strand	93-101	9	3
β-strand	109-110	2	3
β-strand	114-116	3	3
β-strand	117-118	2	2
α-helix	122-123	2
β-strand	124	1	4
α-helix	125-126	2
β-strand	127-131	5	5
α-helix	135-137	3
β-strand	138-139	2	5
β-strand	142-152	11	5
β-strand	153	1	4
β-strand	158-161	4	6
α-helix	162-164	3
β-strand	170-172	3	5
α-helix	173-175	3
β-strand	176-177	2	5
β-strand	183-192	10	5
α-helix	193-195	3
β-strand	202-207	6	6
α-helix	208-210	3
β-strand	212-217	6	6

Chain I: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	11-12	2	8
β-strand	18-25	8	7
β-strand	34-41	8	9
β-strand	48-54	7	9
β-strand	59-61	3	9
α-helix	63-68	6
β-strand	69-74	6	7
β-strand	79-84	6	7
α-helix	89-91	3
β-strand	93-101	9	9
β-strand	109-110	2	9
β-strand	114-116	3	9
β-strand	117-118	2	8
α-helix	122-123	2
β-strand	124	1	10
β-strand	127-131	5	11
α-helix	135-137	3
β-strand	138-139	2	11
β-strand	142-152	11	11
β-strand	153	1	10
β-strand	158-161	4	12
α-helix	162-164	3
β-strand	166	1	12
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	193-195	3
β-strand	202-207	6	12
α-helix	208-210	3
β-strand	212-217	6	12

Chain L: 18 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	13
β-strand	10-14	5	14
β-strand	19-27	9	13
α-helix	43-59	17
α-helix	62-68	7
α-helix	78-84	7
α-helix	89-99	11
α-helix	100-104	5
α-helix	105-108	4
α-helix	113-135	23
α-helix	153-164	12
α-helix	166-175	10
α-helix	177-192	16
β-strand	199-203	5	14
β-strand	210-214	5	14
β-strand	218-219	2	14
β-strand	227-232	6	13
β-strand	235-240	6	13
α-helix	245-247	3
β-strand	249-255	7	14
α-helix	261	1
β-strand	262-263	2	14
β-strand	267-272	6	14
β-strand	276	1	15
α-helix	277-278	2
β-strand	279-283	5	16
α-helix	284-286	3
α-helix	287-291	5
β-strand	294-304	11	16
β-strand	305	1	15
β-strand	310-315	6	17
β-strand	318-319	2	17
α-helix	320	1
β-strand	324-328	5	16
α-helix	329-332	4
β-strand	338-347	10	16
α-helix	348-352	5
β-strand	356-362	7	17
β-strand	370-375	6	17

Chain M: 18 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	18
β-strand	10-14	5	19
β-strand	19-27	9	18
α-helix	47-59	13
α-helix	62-66	5
α-helix	78-84	7
α-helix	89-99	11
α-helix	100-104	5
α-helix	105-107	3
α-helix	113-135	23
α-helix	154-164	11
α-helix	166-175	10
α-helix	177-192	16
β-strand	199-203	5	19
β-strand	210-214	5	19
β-strand	218-219	2	19
β-strand	227-232	6	18
β-strand	235-240	6	18
α-helix	245-247	3
β-strand	249-255	7	19
α-helix	261	1
β-strand	262-263	2	19
β-strand	267-272	6	19
β-strand	276	1	20
α-helix	277-278	2
β-strand	279-283	5	21
α-helix	284-286	3
α-helix	287-291	5
β-strand	294-304	11	21
β-strand	305	1	20
β-strand	310-315	6	22
β-strand	318-319	2	22
α-helix	320	1
β-strand	324-328	5	21
α-helix	329-332	4
β-strand	338-347	10	21
α-helix	348-352	5
β-strand	356-362	7	22
β-strand	370-375	6	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab Heavy chain	H, I	protein	227	Homo sapiens	P0DOX5 (AlphaFold model)
Interleukin-10,Fab light chain	L, M	protein	379	Homo sapiens	P22301 (AlphaFold model)

Sequence of entity 1 (H, I), FASTA

>8SVE_1 Fab Heavy chain (chains H, I)
QVTLRESGPALVKPTQTLTLTCTFSGFSLSTSGMSVGWIRQPPGKALEWLADIWWDDKKD
YNPSLKSRLTISKDTSANQVVLKVTNMDPADTATYYCARSMITNWYFDVWGAGTTVTVSS
ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTH

Sequence of entity 2 (L, M), FASTA

>8SVE_2 Interleukin-10,Fab light chain (chains L, M)
DIQMTQSPSTLSASVGDRVTITCKAQLSSPGQGTQSENSCTHFPGNLPNMLRDLRDAFSR
VKTFFQMKDQLDNLLLKESLLEDFKGYLGCQALSEMIQFYLEEVMPQAENQDPDIKAHVN
SLGENLKTLRLRLRRCHRFLPCENGGGSGGKSKAVEQVKNAFNKLQEKGIYKAMSEFDIF
INYIEAYMTMKIRNVGYMHWYQQKPGKAPKLLIYDTSKLASGVPSRFSGSGSGTAFTLTI
SSLQPDDFATYYCFQGSGYPFTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCL
LNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACE
VTHQGLSSPVTKSFNRGEC

Primary citation

A novel interleukin-10 antibody graft to treat inflammatory bowel disease. DiDonato, M., Simpson, C.T., Vo, T. et al. Structure (2025) 33:475-488.e7. DOI 10.1016/j.str.2024.12.010 · PubMed

Other PDB entries of the same protein (UniProt P0DOX5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6YT7 1.55 Å, Glycosylated knob/dummy-hole fc fragment
6YTB 1.65 Å, Glycosylated knob/dummy-hole/dummy fc fragment
6ARP 1.7 Å, Structure of a mutant Cetuximab Fab fragment
1N0X 1.8 Å, Crystal Structure of a Broadly Neutralizing Anti-HIV-1 Antibody in Complex with a…
6UOE 1.8 Å, 3-25 Fab germline-reversion variant bound to an HCMV gB-derived peptide
8ECV 1.81 Å, Bovine Fab 2F12
6G1E 1.88 Å, BEAT Fc with improved heterodimerization (Q3A-D84.4Q)
5W5L 1.9 Å, Crystal structure of human IgG1-Sigma Fc fragment
6UBI 1.9 Å, N123-VRC34.05 HIV neutralizing antibody in complex with HIV fusion peptide residue 512-519
6DKJ 1.95 Å, human GIPR ECD and Fab complex
6MSY 2.0 Å, Anti-HIV-1 Fab Fab 2G12 + Man4 re-refinement
6UGW 2.0 Å, Crystal structure of the Fc fragment of PF06438179/GP1111 an infliximab biosimilar in a…

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