7YZJ: FAB

FAB in complex with antigenic peptide of interleukin-2. Determined by X-ray diffraction at 2.6 Å resolution. Released 1 Feb 2023.

Method: X-ray diffraction
Resolution: 2.6 Å
Organisms: Mus musculus, Homo sapiens
Chains: 3
Atoms: 3,507
Mol. weight: 49.11 kDa
Released: 1 Feb 2023

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

Secondary structure: helices and β-sheets

7YZJ contains 13 α-helices and 46 β-strands across 3 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 E: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	66-71	6

Chain H: 5 helices, 22 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	34-39	7	9
β-strand	45-52	8	9
β-strand	57-59	3	9
α-helix	64-66	3
β-strand	67-72	6	7
β-strand	77-82	6	7
α-helix	84-86	3
β-strand	88-95	8	9
β-strand	102-103	2	9
β-strand	107-109	3	9
β-strand	110-111	2	8
α-helix	115-116	2
β-strand	117	1	10
α-helix	118-119	2
β-strand	120-124	5	11
β-strand	137-147	11	11
β-strand	148	1	10
β-strand	153-157	4	12
β-strand	166	1	12
β-strand	171-179	9	11
β-strand	184-194	11	11
β-strand	207-212	6	12
α-helix	213-215	3
β-strand	217-222	6	12

Chain L: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-14	5	2
β-strand	19-25	7	1
β-strand	27C	1	3
β-strand	31	1	3
β-strand	33-38	6	2
β-strand	45-49	5	2
β-strand	53-54	2	2
α-helix	55	1
β-strand	62-67	6	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	84-90	7	2
β-strand	97-98	2	2
β-strand	99	1	1
β-strand	102-107	6	2
β-strand	111	1	4
α-helix	112-113	2
β-strand	114-118	5	5
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	5
β-strand	140	1	4
β-strand	145-150	6	6
β-strand	153-155	3	6
β-strand	159-163	5	5
β-strand	173-182	10	5
α-helix	183-187	5
β-strand	191-197	7	6
α-helix	204	1
β-strand	205-210	6	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Light chain of FAB fragment	L	protein	219	Mus musculus
Heavy chain of FAB fragment	H	protein	220	Mus musculus
Antigenic peptide	E	protein	9	Homo sapiens	P60568 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>7YZJ_1 Light chain of FAB fragment (chains L)
DVQMTQTPLTLSVTIGQPASISCESSQSLLYSNGKTYLNWLLQRPGQSPKRLIYLVSKLD
SGVPDRFTGSGSGTDFTLRISRVEAEDLGVYYCVQGTHFPRTFGGGTKLEIKRADAAPTV
SIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSM
SSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 2 (H), FASTA

>7YZJ_2 Heavy chain of FAB fragment (chains H)
GVQLQESGPGLVKPSQSLSLTCTVTGYSITSDYAWNWIRQFPGNKLEWMGYITYSGSTGY
NPSLKSRISITRDTSKNQFFLQLNSVTTEDTATYYCASYDDYTWFTYWGQGTLVTVSAAK
TTPPSVFPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLY
TLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRDC

Sequence of entity 3 (E), FASTA

>7YZJ_3 Antigenic peptide (chains E)
KPLEEVLNL

Primary citation

Three-Dimensional Structure of Fab Fragment of Monoclonal Antibody LNKB-2 Complexed with Antigenic Nonapeptide from Human Interleukin-2. Pletnev, V., Pletneva, N., Goryacheva, E. et al. Russ J Bioorg Chem (2023).

Other PDB entries of the same protein (UniProt P60568 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8SOZ 1.64 Å, Structure of the complex formed by human interleukin-2 and scFv 602
8SOW 1.71 Å, Structure of the complex formed by human interleukin-2 and scFv F10
7M2G 1.79 Å, INTERLEUKIN-2 (human) mutant P65K, C125S
4NEJ 1.92 Å, Small molecular fragment bound to crystal contact interface of Interleukin-2
4NEM 1.93 Å, Small molecular fragment bound to crystal contact interface of Interleukin-2
1M48 1.95 Å, Crystal Structure of Human IL-2 Complexed with (R)-N-[2-[1-(Aminoiminomethyl)-3-piperidin…
5LQB 1.95 Å, Complex structure of human IL2 mutant, Proleukin, with Fab fragment of NARA1 antibody
1M47 1.99 Å, Crystal Structure of Human Interleukin-2
1M49 2.0 Å, Crystal Structure of Human Interleukin-2 Complexed with SP-1985
1M4B 2.15 Å, Crystal Structure of Human Interleukin-2 K43C Covalently Modified at C43 with…
1M4A 2.18 Å, Crystal Structure of Human Interleukin-2 Y31C Covalently Modified at C31 with…
1NBP 2.2 Å, Crystal Structure Of Human Interleukin-2 Y31C Covalently Modified At C31 With…

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