7UM3: Fab

Crystal structure of a Fab in complex with a peptide derived from the LAG-3 D1 domain loop insertion. Determined by X-ray diffraction at 2.4 Å resolution. Released 7 Sept 2022.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 6
Atoms: 6,978
Mol. weight: 100.19 kDa
Released: 7 Sept 2022

Explore 7UM3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7UM3 contains 32 α-helices and 90 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: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	12
β-strand	11-12	2	13
β-strand	18-25	8	12
β-strand	32-39	8	14
β-strand	46-52	7	14
β-strand	57-59	3	14
α-helix	61-63	3
β-strand	67-72	6	12
β-strand	77-82	6	12
α-helix	84-86	3
β-strand	88-97	10	14
β-strand	100C-100D	2	14
β-strand	103	1	14
β-strand	107-109	3	14
β-strand	110-111	2	13
β-strand	117	1	15
α-helix	118-119	2
β-strand	120-124	5	16
β-strand	135-145	11	16
β-strand	146	1	15
β-strand	151-154	4	17
α-helix	155-157	3
β-strand	159	1	17
β-strand	163-165	3	16
α-helix	166-168	3
β-strand	169-170	2	16
β-strand	176-185	10	16
α-helix	186-188	3
β-strand	195-200	6	17
α-helix	201-203	3
β-strand	205-210	6	17

Chain I: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	1
β-strand	11-12	2	2
β-strand	18-25	8	1
β-strand	31-39	9	3
β-strand	46-52	7	3
β-strand	57-59	3	3
α-helix	61-63	3
β-strand	67-72	6	1
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-97	10	3
β-strand	100C-100D	2	3
β-strand	103	1	3
β-strand	107-109	3	3
β-strand	110-111	2	2
β-strand	117	1	4
α-helix	118-119	2
β-strand	120-124	5	5
α-helix	125-127	3
β-strand	135-145	11	5
β-strand	146	1	4
β-strand	151-154	4	6
α-helix	155-157	3
β-strand	159	1	6
β-strand	163-165	3	5
α-helix	166-168	3
β-strand	169-170	2	5
β-strand	176-185	10	5
α-helix	186-188	3
β-strand	195-200	6	6
α-helix	201-203	3
β-strand	205-210	6	6

Chain L: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-7	4	18
β-strand	10-13	4	19
β-strand	19-25	7	18
β-strand	33-38	6	19
β-strand	45-49	5	19
β-strand	53-54	2	19
α-helix	55	1
β-strand	62-66	5	18
β-strand	70-75	6	18
α-helix	80-82	3
β-strand	85-90	6	19
α-helix	96	1
β-strand	97-98	2	19
β-strand	102-106	5	19
β-strand	111	1	20
α-helix	112-113	2
β-strand	114-118	5	21
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	21
β-strand	140	1	20
β-strand	145-150	6	22
β-strand	153-154	2	22
β-strand	159-163	5	21
α-helix	164-167	4
β-strand	173-182	10	21
α-helix	183-186	4
β-strand	191-197	7	22
β-strand	205-210	6	22

Chain M: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	7
β-strand	10-13	4	8
β-strand	19-25	7	7
β-strand	33-38	6	8
β-strand	45-49	5	8
β-strand	53-54	2	8
α-helix	55	1
β-strand	62-66	5	7
β-strand	70-75	6	7
α-helix	80-82	3
β-strand	84-90	7	8
α-helix	96	1
β-strand	97-98	2	8
β-strand	102-106	5	8
β-strand	111	1	9
α-helix	112-113	2
β-strand	114-118	5	10
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	10
β-strand	140	1	9
β-strand	144-150	7	11
β-strand	153-154	2	11
β-strand	159-163	5	10
α-helix	164-167	4
β-strand	173-182	10	10
α-helix	183-187	5
β-strand	191-198	8	11
β-strand	205-210	6	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab heavy chain	H, I	protein	231	Homo sapiens
Fab light chain	L, M	protein	214	Homo sapiens
D1 domain loop peptide from Lymphocyte activation gene 3 protein	A, B	protein	16	Homo sapiens	P18627 (AlphaFold model)

Sequence of entity 1 (H, I), FASTA

>7UM3_1 Fab heavy chain (chains H, I)
QVQLQQWGAGLLKPSETLSLTCAVYGGSFSDYYWNWIRQPPGKGLEWIGEINHNGNTNSN
PSLKSRVTLSLDTSKNQFSLKLRSVTAADTAVYYCAFGYSDYEYNWFDPWGQGTLVTVSS
ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCGGHHHHHH

Sequence of entity 2 (L, M), FASTA

>7UM3_2 Fab light chain (chains L, M)
EIVLTQSPATLSLSPGERATLSCRASQSISSYLAWYQQKPGQAPRLLIYDASNRATGIPA
RFSGSGSGTDFTLTISSLEPEDFAVYYCQQRSNWPLTFGQGTNLEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (A, B), FASTA

>7UM3_3 D1 domain loop peptide from Lymphocyte activation gene 3 protein (chains A, B)
PGPHPAAPSSWGPRPR

Primary citation

Preclinical Characterization of Relatlimab, a Human LAG-3-Blocking Antibody, Alone or in Combination with Nivolumab. Thudium, K., Selby, M., Zorn, J.A. et al. Cancer Immunol Res (2022) 10:1175-1189. DOI 10.1158/2326-6066.CIR-22-0057 · PubMed

Other PDB entries of the same protein (UniProt P18627 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7TZH 2.43 Å, Structure of human LAG3 domains 3-4 in complex with antibody single chain-variable…
9BF9 3.4 Å, Human LAG-3-HLA-DR1 complex
8SR0 3.53 Å, CryoEM structure of a therapeutic antibody (favezelimab) bound to human LAG3 local refined
8SO3 3.61 Å, CryoEM structure of a therapeutic antibody (favezelimab) bound to human LAG3
7TZG 3.71 Å, Structure of human LAG3 in complex with antibody single-chain variable fragment

Browse structure collections

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