3LKJ: CD40 ligand

Name: PDB 3LKJ: Small Molecule Inhibition of the TNF Family Cyokine CD40 Ligand Through a Subunit Fracture Mechanism
Published: 2011-02-02
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: cytokine

Small Molecule Inhibition of the TNF Family Cyokine CD40 Ligand Through a Subunit Fracture Mechanism. Determined by X-ray diffraction at 2.5 Å resolution. Released 2 Feb 2011.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,226
Mol. weight: 48.14 kDa
Ligands: LKJ, NAG
Released: 2 Feb 2011

Explore 3LKJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3LKJ contains 5 α-helices and 38 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: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	123-129	7	1
β-strand	137	1	2
β-strand	139-141	3	1
β-strand	147-148	2	1
β-strand	153-156	4	2
β-strand	160-163	4	2
β-strand	167-177	11	1
α-helix	187-188	2
β-strand	189-196	8	2
β-strand	203-210	8	2
β-strand	221-231	11	1
β-strand	236-241	6	2
α-helix	244-246	3
β-strand	247	1	1
β-strand	255-260	6	1

Chain B: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	123-128	6	3
β-strand	137	1	4
α-helix	138-139	2
β-strand	140-141	2	3
β-strand	147-148	2	3
β-strand	153-156	4	4
β-strand	160-163	4	4
β-strand	167-178	12	3
β-strand	189-196	8	4
β-strand	203-210	8	4
β-strand	220-231	12	3
β-strand	236-241	6	4
α-helix	244-246	3
β-strand	247	1	3
β-strand	255-260	6	3

Chain C: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	123-129	7	5
β-strand	137	1	6
β-strand	139-141	3	5
β-strand	153-156	4	6
β-strand	160-163	4	6
β-strand	167-177	11	5
β-strand	189-197	9	6
β-strand	200-210	11	6
β-strand	221-231	11	5
β-strand	236-241	6	6
α-helix	244-246	3
β-strand	247	1	5
β-strand	255-260	6	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CD40 ligand	A, B, C	protein	141	Homo sapiens	P29965 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>3LKJ_1 CD40 ligand (chains A, B, C)
QIAAHVISEASSKTTSVLQWAEKGYYTMSNNLVTLENGKQLTVKRQGLYYIYAQVTFCSN
REASSQAPFIASLCLKSPGRFERILLRAANTHSSAKPCGQQSIHLGGVFELQPGASVFVN
VTDPSQVSHGTGFTSFGLLKL

Ligands and cofactors

ID	Name	Formula	Copies
LKJ	(2R)-{[(2'-[(biphenyl-3-ylmethyl)carbamoyl]-6'-{[(2R)-2-(pyrrolidin-1-ylmethyl)…	C53 H60 N8 O6	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6

Primary citation

Small Molecule Inhibition of the TNF Family Cytokine CD40 Ligand through a Subunit Fracture Mechanism. Silvian, L.F., Friedman, J.E., Strauch, K. et al. ACS Chem Biol (2011) 6:636-647. DOI 10.1021/cb2000346 · PubMed

Other PDB entries of the same protein (UniProt P29965 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6W9G 1.82 Å, Crystal Structure of the Fab fragment of humanized 5c8 antibody containing the…
1ALY 2.0 Å, Crystal structure of human CD40 ligand
7SGM 2.0 Å, Crystal structure of a Fab variant containing a fluorescent noncanonical amino acid with…
6BRB 2.82 Å, Novel non-antibody protein scaffold targeting CD40L
1I9R 3.1 Å, Structure of CD40L in complex with the FAB fragment of humanized 5C8 antibody
9I5N 3.4 Å, Single particle cryo electron microscopy of a Fab fragment bound to recombinant human…
3QD6 3.5 Å, Crystal structure of the CD40 and CD154 (CD40L) complex

Browse structure collections

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