5Y9J: BAFF

BAFF in complex with belimumab. Determined by X-ray diffraction at 2.05 Å resolution. Released 21 Feb 2018.

Method: X-ray diffraction
Resolution: 2.05 Å
Organism: Homo sapiens
Chains: 3
Atoms: 4,830
Mol. weight: 64.8 kDa
Released: 21 Feb 2018

Explore 5Y9J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5Y9J contains 17 α-helices and 58 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 A: 0 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	146-151	6	12
β-strand	158-160	3	13
β-strand	163-165	3	13
β-strand	168-174	7	12
β-strand	178-181	4	14
β-strand	184-187	4	14
β-strand	191-201	11	12
β-strand	207-215	9	14
β-strand	226-235	10	14
β-strand	243-253	11	12
β-strand	258-262	5	14
β-strand	263	1	13
β-strand	270	1	12
β-strand	278-283	6	12

Chain H: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	7
α-helix	7-9	3
β-strand	10-12	3	8
β-strand	18-24	7	7
β-strand	33-39	7	8
β-strand	45-51	7	8
β-strand	59-60	2	8
β-strand	68-73	6	7
α-helix	74-76	3
β-strand	78-83	6	7
α-helix	88-90	3
β-strand	92-99	8	8
β-strand	113	1	8
β-strand	117-121	5	8
α-helix	125-126	2
β-strand	127	1	9
α-helix	128-129	2
β-strand	130-134	5	10
β-strand	145-155	11	10
β-strand	156	1	9
β-strand	161-164	4	11
α-helix	165-167	3
β-strand	173-175	3	10
α-helix	176-178	3
β-strand	179-180	2	10
β-strand	186-195	10	10
α-helix	196-198	3
β-strand	205-210	6	11
α-helix	211-213	3
β-strand	215-220	6	11

Chain L: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	1
β-strand	9-13	5	2
β-strand	18-23	6	1
α-helix	25-28	4
β-strand	33-37	5	2
β-strand	44-47	4	2
β-strand	48	1	3
β-strand	52	1	3
β-strand	61-66	6	1
β-strand	69-74	6	1
α-helix	79-81	3
β-strand	83-89	7	2
β-strand	98-99	2	2
β-strand	103-108	6	2
α-helix	110-112	3
β-strand	113	1	4
α-helix	114-115	2
β-strand	116-120	5	5
α-helix	121-123	3
α-helix	124-128	5
β-strand	132-141	10	5
β-strand	142	1	4
β-strand	147-152	6	6
β-strand	155-157	3	6
β-strand	161-163	3	5
α-helix	164-166	3
β-strand	167-168	2	5
β-strand	174-182	9	5
α-helix	184-189	6
β-strand	193-199	7	6
β-strand	202-208	7	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
belibumab light chain	L	protein	214	Homo sapiens
belimumab heavy chain	H	protein	235	Homo sapiens
Tumor necrosis factor ligand superfamily member 13B	A	protein	152	Homo sapiens	Q9Y275 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>5Y9J_1 belibumab light chain (chains L)
SSELTQDPAVSVALGQTVRVTCQGDSLRSYYASWYQQKPGQAPVLVIYGKNNRPSGIPDR
FSGSSSGNTASLTITGAQAEDEADYYCSSRDSSGNHWVFGGGTELTVLGQPKAAPSVTLF
PPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYL
SLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 2 (H), FASTA

>5Y9J_2 belimumab heavy chain (chains H)
QVQLQQSGAEVKKPGSSVRVSCKASGGTFNNNAINWVRQAPGQGLEWMGGIIPMFGTAKY
SQNFQGRVAITADESTGTASMELSSLRSEDTAVYYCARSRDLLLFPHHALSPWGRGTMVT
VSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVL
QSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHHHHHH

Sequence of entity 3 (A), FASTA

>5Y9J_3 Tumor necrosis factor ligand superfamily member 13B (chains A)
AVQGPEETVTQDCLQLIADSETPTIQKGSYTFVPWLLSFKRGSALEEKENKILVKETGYF
FIYGQVLYTDKTYAMGHLIQRKKVHVFGDELSLVTLFRCIQNMPETLPNNSCYSAGIAKL
EEGDELQLAIPRENAQISLDGDVTFFGALKLL

Primary citation

BAFF-neutralizing interaction of belimumab related to its therapeutic efficacy for treating systemic lupus erythematosus. Shin, W., Lee, H.T., Lim, H. et al. Nat Commun (2018) 9:1200-1200. DOI 10.1038/s41467-018-03620-2 · PubMed

Other PDB entries of the same protein (UniProt Q9Y275 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1KXG 2.0 Å, The 2.0 Ang Resolution Structure of BLyS, B Lymphocyte Stimulator.
4ZCH 2.43 Å, Single-chain human APRIL-BAFF-BAFF Heterotrimer
1OQE 2.5 Å, Crystal structure of sTALL-1 with BAFF-R
8ZUJ 2.58 Å, Pentagonal cluster of BAFF-BAFFR ectodomain complex
1OQD 2.6 Å, Crystal structure of sTALL-1 and BCMA
1KD7 2.8 Å, Crystal structure of an extracellular domain fragment of human BAFF
6FXN 2.9 Å, Crystal structure of human BAFF in complex with Fab fragment of anti-BAFF antibody…
1JH5 3.0 Å, Crystal Structure of sTALL-1 of TNF family ligand
1OSG 3.0 Å, Complex between BAFF and a BR3 derived peptide presented in a beta-hairpin scaffold
3V56 3.0 Å, Re-refinement of PDB entry 1OSG - Complex between BAFF and a BR3 derived peptide…
4V46 3.3 Å, Crystal structure of the BAFF-BAFF-R complex

Browse structure collections

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