6W9G: CD40 ligand

Crystal Structure of the Fab fragment of humanized 5c8 antibody containing the fluorescent non-canonical amino acid L-(7-hydroxycoumarin-4-yl)ethylglycine in complex with CD40L at pH 6.8. Determined by X-ray diffraction at 1.82 Å resolution. Released 23 Dec 2020.

Method: X-ray diffraction
Resolution: 1.82 Å
Organism: Homo sapiens
Chains: 9
Atoms: 14,802
Mol. weight: 198.47 kDa
Ligands: ETE, TMO
Released: 23 Dec 2020

Explore 6W9G in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6W9G contains 61 α-helices and 177 β-strands across 9 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: 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	167-179	13	1
β-strand	189-196	8	2
β-strand	203-210	8	2
α-helix	211-213	3
β-strand	219-231	13	1
β-strand	236-241	6	2
α-helix	244-246	3
β-strand	247	1	1
β-strand	255-260	6	1

Chain C: 3 helices, 13 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	147-148	2	5
β-strand	153-156	4	6
β-strand	160-163	4	6
β-strand	167-179	13	5
α-helix	187-188	2
β-strand	189-196	8	6
β-strand	203-210	8	6
α-helix	211-213	3
β-strand	219-231	13	5
β-strand	236-241	6	6
α-helix	244-246	3
β-strand	247	1	5
β-strand	255-260	6	5

Chain H: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	7
α-helix	7-9	3
β-strand	10-12	3	8
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	33-39	7	8
β-strand	45-51	7	8
β-strand	58-60	3	8
α-helix	62-64	3
β-strand	68-73	6	7
β-strand	78-83	6	7
α-helix	88-90	3
β-strand	92-100	9	8
β-strand	104-108	5	8
β-strand	112-116	5	8
β-strand	122	1	9
α-helix	123-125	3
β-strand	126-129	4	10
β-strand	140-147	8	10
β-strand	151	1	9
β-strand	156-159	4	11
α-helix	160-162	3
β-strand	164	1	11
β-strand	168-170	3	10
α-helix	171-173	3
β-strand	174-175	2	12
β-strand	181-182	2	12
β-strand	183-190	8	10
α-helix	191-193	3
β-strand	199-205	7	11
α-helix	206-208	3
β-strand	210-216	7	11

Chain K: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	19
α-helix	7-9	3
β-strand	10-12	3	20
β-strand	18-25	8	19
α-helix	29-31	3
β-strand	33-39	7	20
β-strand	45-51	7	20
β-strand	58-60	3	20
α-helix	62-64	3
β-strand	68-73	6	19
β-strand	78-83	6	19
α-helix	88-90	3
β-strand	92-100	9	20
β-strand	104-108	5	20
β-strand	112-116	5	20
β-strand	122	1	21
α-helix	123-124	2
β-strand	125-129	5	22
β-strand	140-150	11	22
β-strand	151	1	21
β-strand	156-159	4	23
α-helix	160-162	3
β-strand	164	1	23
β-strand	168-170	3	22
α-helix	171-173	3
β-strand	174-175	2	22
β-strand	181-190	10	22
α-helix	191-193	3
β-strand	200-205	6	23
α-helix	206-208	3
β-strand	210-215	6	23

Chain L: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	13
β-strand	10-13	4	14
β-strand	19-25	7	13
β-strand	30	1	15
β-strand	35	1	15
β-strand	37-42	6	14
β-strand	49-53	5	14
β-strand	57-58	2	14
α-helix	59	1
β-strand	66-71	6	13
β-strand	74-79	6	13
α-helix	84-86	3
β-strand	88-94	7	14
α-helix	100	1
β-strand	101	1	8
β-strand	102	1	14
β-strand	106-110	5	14
β-strand	115	1	16
α-helix	116-117	2
β-strand	118-122	5	17
α-helix	123-125	3
α-helix	126-129	4
β-strand	133-143	11	17
β-strand	144	1	16
β-strand	149-154	6	18
β-strand	157-158	2	18
β-strand	163-167	5	17
α-helix	168-171	4
β-strand	177-186	10	17
α-helix	187-191	5
β-strand	195-201	7	18
β-strand	209-214	6	18

Chain M: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	24
β-strand	10-13	4	25
β-strand	19-25	7	24
β-strand	30	1	26
β-strand	35	1	26
β-strand	37-42	6	25
β-strand	49-53	5	25
β-strand	57-58	2	25
α-helix	59	1
β-strand	66-71	6	24
β-strand	74-79	6	24
α-helix	84-86	3
β-strand	88-94	7	25
α-helix	100	1
β-strand	101	1	20
β-strand	102	1	25
β-strand	106-110	5	25
β-strand	115	1	27
α-helix	116-117	2
β-strand	118-122	5	28
α-helix	123-125	3
α-helix	126-130	5
β-strand	133-143	11	28
β-strand	144	1	27
β-strand	149-154	6	29
β-strand	157-158	2	29
α-helix	159	1
β-strand	163-167	5	28
α-helix	168-171	4
β-strand	177-186	10	28
α-helix	187-191	5
β-strand	195-201	7	29
β-strand	209-214	6	29

Chain X: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	30
α-helix	7-9	3
β-strand	10-12	3	31
β-strand	18-25	8	30
α-helix	29-31	3
β-strand	33-39	7	31
β-strand	45-52	8	31
β-strand	57-60	4	31
α-helix	62-64	3
β-strand	68-73	6	30
α-helix	74-76	3
β-strand	78-83	6	30
α-helix	88-90	3
β-strand	92-100	9	31
β-strand	104-108	5	31
β-strand	112-116	5	31
β-strand	122	1	32
α-helix	123-124	2
β-strand	125-129	5	33
β-strand	140-150	11	33
β-strand	151	1	32
β-strand	156-159	4	34
α-helix	160-162	3
β-strand	168-170	3	33
α-helix	171-173	3
β-strand	174-175	2	33
β-strand	181-190	10	33
α-helix	193-196	4
β-strand	199-205	7	34
α-helix	206-208	3
β-strand	210-216	7	34

Chain Y: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	35
β-strand	10-13	4	36
β-strand	19-25	7	35
β-strand	30	1	37
β-strand	35	1	37
β-strand	37-42	6	36
β-strand	49-53	5	36
β-strand	57-58	2	36
α-helix	59	1
β-strand	66-71	6	35
β-strand	74-79	6	35
α-helix	84-86	3
β-strand	88-94	7	36
α-helix	100	1
β-strand	101	1	31
β-strand	102	1	36
β-strand	106-110	5	36
β-strand	115	1	38
α-helix	116-117	2
β-strand	118-122	5	39
α-helix	123-125	3
α-helix	126-131	6
β-strand	133-143	11	39
β-strand	144	1	38
β-strand	149-154	6	40
β-strand	157-158	2	40
α-helix	159	1
β-strand	163-167	5	39
α-helix	168-171	4
β-strand	177-186	10	39
α-helix	187-191	5
β-strand	195-201	7	40
β-strand	209-214	6	40

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CD40 ligand	A, B, C	protein	146	Homo sapiens	P29965 (AlphaFold model)
5c8* Fab (heavy chain)	H, K, X	protein	226	Homo sapiens
5c8* Fab (light chain)	L, M, Y	protein	218	Homo sapiens

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

>6W9G_1 CD40 ligand (chains A, B, C)
GDQNPQIAAHVISEASSKTTSVLQWAEKGYYTMSNNLVTLENGKQLTVKRQGLYYIYAQV
TFCSNREASSQAPFIASLCLKSPGRFERILLRAANTHSSAKPCGQQSIHLGGVFELQPGA
SVFVNVTDPSQVSHGTGFTSFGLLKL

Sequence of entity 2 (H, K, X), FASTA

>6W9G_2 5c8* Fab (heavy chain) (chains H, K, X)
QVQLVQSGAEVVKPGASVKLSCKASGYIFTSYYMYWVKQAPGQGLEWIGEINPSNGDTNF
NEKFKSKATLTVDKSASTAYMELSSLRSEDTAVYYCTRSDGRNDMDSWGQGTLVTVSSAS
TKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGL
YSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Sequence of entity 3 (L, M, Y), FASTA

>6W9G_3 5c8* Fab (light chain) (chains L, M, Y)
DIVLTQSPATLSVSPGERATISCRASQRVSSSTYSYMHWYQQKPGQPPKLLIKYASNLES
GVPARFSGSGSGTDFTLTISSVEPEDFATYYCQHSWEXPPTFGGGTKLEIKRTVAAPSVF
IFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS
STLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
ETE	2-{2-[2-2-(methoxy-ethoxy)-ethoxy]-ethoxy}-ethanol	C9 H20 O5	3
TMO	trimethylamine oxide	C3 H9 N O	21

Water and common crystallization additives (1PE, TRS, PEG) are not listed.

Primary citation

Structural Insights into How Protein Environments Tune the Spectroscopic Properties of a Noncanonical Amino Acid Fluorophore. Henderson, J.N., Simmons, C.R., Fahmi, N.E. et al. Biochemistry (2020) 59:3401-3410. DOI 10.1021/acs.biochem.0c00474 · PubMed

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

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…
3LKJ 2.5 Å, Small Molecule Inhibition of the TNF Family Cyokine CD40 Ligand Through a Subunit…
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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