1I9R: CD40L

Structure of CD40L in complex with the FAB fragment of humanized 5C8 antibody. Determined by X-ray diffraction at 3.1 Å resolution. Released 20 Mar 2002.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 9
Atoms: 13,170
Mol. weight: 189.19 kDa
Ligands: ZN
Released: 20 Mar 2002

Explore 1I9R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1I9R contains 53 α-helices and 184 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.

Chain A: 2 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	123-129	7	1
β-strand	137	1	2
α-helix	138	1
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
β-strand	219-225	7	1
β-strand	228-231	4	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, 14 β-strands

Element	Residues	Length	Sheet
β-strand	123-129	7	3
β-strand	137	1	4
α-helix	138	1
β-strand	139-141	3	3
β-strand	147-148	2	3
β-strand	153-156	4	4
β-strand	160-163	4	4
β-strand	167-179	13	3
β-strand	189-196	8	4
β-strand	204-210	7	4
β-strand	219-225	7	3
β-strand	228-231	4	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: 2 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	123-129	7	5
β-strand	137	1	6
α-helix	138	1
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
β-strand	189-195	7	6
β-strand	203-210	8	6
β-strand	219-225	7	5
β-strand	228-231	4	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, 22 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	34-39	6	8
β-strand	45-51	7	8
β-strand	58-60	3	8
α-helix	62-64	3
β-strand	70-73	4	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
β-strand	125-129	5	10
α-helix	133-135	3
β-strand	140-150	11	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	175	1	10
β-strand	181-190	10	10
α-helix	193-196	4
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
β-strand	10-12	3	20
β-strand	17-25	9	19
α-helix	29-31	3
β-strand	34-39	6	20
β-strand	45-51	7	20
β-strand	58-60	3	20
α-helix	62-64	3
β-strand	71-73	3	19
α-helix	74-76	3
β-strand	78-84	7	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
β-strand	125-129	5	22
α-helix	133-135	3
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	175	1	22
β-strand	181-190	10	22
α-helix	193-196	4
β-strand	199-205	7	23
α-helix	206-208	3
β-strand	210-216	7	23

Chain L: 7 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	12
β-strand	7	1	13
β-strand	10-13	4	14
β-strand	19-24	6	13
β-strand	25	1	12
β-strand	30	1	15
β-strand	35	1	15
β-strand	37-42	6	14
α-helix	47-48	2
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	89-94	6	14
α-helix	100	1
β-strand	102	1	14
β-strand	106-110	5	14
α-helix	111	1
β-strand	115	1	16
β-strand	118-122	5	17
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	163-164	2	17
β-strand	167	1	17
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: 7 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	24
β-strand	7	1	25
β-strand	10-13	4	26
β-strand	19-24	6	25
β-strand	25	1	24
β-strand	30	1	27
β-strand	35	1	27
β-strand	37-42	6	26
α-helix	47-48	2
β-strand	49-53	5	26
β-strand	57-58	2	26
α-helix	59	1
β-strand	68-71	4	25
β-strand	74-79	6	25
α-helix	84-86	3
β-strand	89-94	6	26
α-helix	100	1
β-strand	102	1	26
β-strand	106-110	5	26
α-helix	111	1
β-strand	115	1	28
β-strand	118-122	5	29
α-helix	126-129	4
β-strand	133-143	11	29
β-strand	144	1	28
β-strand	149-154	6	30
β-strand	157-158	2	30
β-strand	163-164	2	29
β-strand	167	1	29
β-strand	177-186	10	29
α-helix	187-191	5
β-strand	195-201	7	30
β-strand	209-214	6	30

Chain X: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	31
β-strand	10-12	3	32
β-strand	18-25	8	31
α-helix	29-31	3
β-strand	33-39	7	32
β-strand	45-51	7	32
β-strand	58-60	3	32
α-helix	62-64	3
β-strand	71-73	3	31
β-strand	78-83	6	31
α-helix	88-90	3
β-strand	92-100	9	32
β-strand	104-108	5	32
β-strand	112-116	5	32
β-strand	122	1	33
β-strand	125-129	5	34
α-helix	133-135	3
β-strand	140-150	11	34
β-strand	151	1	33
β-strand	156-159	4	35
α-helix	160-162	3
β-strand	164	1	35
β-strand	168-170	3	34
α-helix	171-173	3
β-strand	175	1	34
β-strand	181-190	10	34
α-helix	193-196	4
β-strand	199-205	7	35
α-helix	206-208	3
β-strand	210-216	7	35

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CD40 ligand	A, B, C	protein	146	Homo sapiens	P29965 (AlphaFold model)
Immunoglobulin H	H, K, X	protein	219	Homo sapiens
Immunoglobulin L	L, M, Y	protein	218	Homo sapiens

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

>1I9R_1 CD40 LIGAND (chains A, B, C)
GDQNPQIAAHVISEASSKTTSVLQWAEKGYYTMSNNLVTLENGKQLTVKRQGLYYIYAQV
TFCSNREASSQAPFIASLCLKSPGRFERILLRAANTHSSAKPCGQQSIHLGGVFELQPGA
SVFVNVTDPSQVSHGTGFTSFGLLKL

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

>1I9R_2 IMMUNOGLOBULIN H (chains H, K, X)
QVQLVQSGAEVVKPGASVKLSCKASGYIFTSYYMYWVKQAPGQGLEWIGEINPSNGDTNF
NEKFKSKATLTVDKSASTAYMELSSLRSEDTAVYYCTRSDGRNDMDSWGQGTLVTVSSAS
TKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGL
YSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

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

>1I9R_3 IMMUNOGLOBULIN L (chains L, M, Y)
DIVLTQSPATLSVSPGERATISCRASQRVSSSTYSYMHWYQQKPGQPPKLLIKYASNLES
GVPARFSGSGSGTDFTLTISSVEPEDFATYYCQHSWEIPPTFGGGTKLEIKRTVAAPSVF
IFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS
STLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	3

Primary citation

Structure of CD40 ligand in complex with the Fab fragment of a neutralizing humanized antibody. Karpusas, M., Lucci, J., Ferrant, J. et al. Structure (2001) 9:321-329. DOI 10.1016/S0969-2126(01)00590-1 · 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…
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
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

About this viewer

MolViewer shows 1I9R directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.