1KD7: Extracellular domain fragment of human BAFF

Crystal structure of an extracellular domain fragment of human BAFF. Determined by X-ray diffraction at 2.8 Å resolution. Released 12 Nov 2002.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 6
Atoms: 6,858
Mol. weight: 111.35 kDa
Released: 12 Nov 2002

Explore 1KD7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1KD7 contains 18 α-helices and 80 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.

Chains A and B: 3 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	146-151	6	1
α-helix	156-157	2
β-strand	158-160	3	2
β-strand	163-165	3	2
α-helix	166-167	2
β-strand	168-174	7	1
β-strand	179-180	2	3
β-strand	185-186	2	3
α-helix	187	1
β-strand	191-201	11	1
β-strand	207-215	9	3
β-strand	226-235	10	3
β-strand	243-253	11	1
β-strand	258-262	5	3
β-strand	263	1	2
β-strand	270	1	1
β-strand	278-283	6	1

Chains C, K, L and M: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	146-151	6	7
α-helix	156-157	2
β-strand	158-160	3	8
β-strand	163-165	3	8
α-helix	166-167	2
β-strand	168-174	7	7
β-strand	179-180	2	8
β-strand	185-186	2	8
α-helix	187	1
β-strand	191-201	11	7
β-strand	207-215	9	8
β-strand	226-235	10	8
β-strand	243-253	11	7
β-strand	258-263	6	8
β-strand	270	1	7
β-strand	278-283	6	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tumor necrosis factor ligand superfamily member 13B	A, B, C, K, L, M	protein	164	Homo sapiens	Q9Y275 (AlphaFold model)

Sequence of entity 1 (A, B, C, K, L, M), FASTA

>1KD7_1 TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13B (chains A, B, C, K, L, M)
EQKLISEEDLNKELQGPEETVTQDCLQLIADSETPTIQKGSYTFVPWLLSFKRGSALEEK
ENKILVKETGYFFIYGQVLYTDKTYAMGHLIQRKKVHVFGDELSLVTLFRCIQNMPETLP
NNSCYSAGIAKLEEGDELQLAIPRENAQISLDGDVTFFGALKLL

Primary citation

Crystal Structure of Extracellular Human BAFF, a TNF Family Member that Stimulates B Lymphocytes. Karpusas, M., Cachero, T.G., Qian, F. et al. J Mol Biol (2002) 315:1145-1154. DOI 10.1006/jmbi.2001.5296 · 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.
5Y9J 2.05 Å, BAFF in complex with belimumab
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
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

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