PiSITE

PDB ID	1ALY	CHAIN	A
Protein name	CD40 LIGAND
Uniprot Accession	P29965
The number of similar proteins	17
The number of binding states	7
The number of binding partners	4

Coloring

Unicolor (beige)

The number of binding partners

Group

Binding state	Binding partners
	1ALY (CHAIN: A)
1	Monomeric state
2	6BRB
3	P29965 P29965
4	P29965 P29965 P25942
5	P29965 P29965 1I9R 1I9R
6	P29965 P29965 P25942 P25942
7	P29965 P29965 7SGM 7SGM 7SGM

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Only interaction residues

#binding
partners

	4
	3
	2
	1
	0

Sequence information

GDQNPQIAAH

VISEASSKTT

SVLQWAEKGY

YTMSNNLVTL

ENGKQLTVKR

QGLYYIYAQV

TFCSNREASS

QAPFIASLCL

KSPGRFERIL

LRAANTHSSA

100

101

KPCGQQSIHL

GGVFELQPGA

SVFVNVTDPS

QVSHGTGFTS

FGLLKL

150

Variants

Residue	AA	Source / dbSNP	Clinical Significance	Allele Frequency (> 0.0001)	AlphaMissense pathogenicity	Disease name
116_GLY	ARG	VAR_017929 -	LP/P	-	0.4836	Immunodeficiency with hyper-IgM, type 1 (HIGM1) [MIM:308230]
116_GLY	SER	VAR_017930 -	LP/P	-	0.2102	Immunodeficiency with hyper-IgM, type 1 (HIGM1) [MIM:308230]
116_GLY	CYS	ClinVar chrX:135736589 rs2148552406	Likely pathogenic	-	0.599	Hyper-IgM syndrome type 1 [MONDO:MONDO:0010626,MedGen:C0398689,OMIM:308230,Orphanet:101088]
123_ALA	GLU	VAR_007514 rs104894778	LP/P	-	0.8963	Immunodeficiency with hyper-IgM, type 1 (HIGM1) [MIM:308230]
123_ALA	GLU	ClinVar chrX:135738536 rs104894778	Pathogenic	-	0.8963	Hyper-IgM syndrome type 1 [MONDO:MONDO:0010626,MedGen:C0398689,OMIM:308230,Orphanet:101088]
123_ALA	VAL	8.3kJPN chrX:135738536 rs104894778	-	0.0002	0.2806	-
125_HIS	ARG	VAR_017926 -	LP/P	-	0.7502	Immunodeficiency with hyper-IgM, type 1 (HIGM1) [MIM:308230]
125_HIS	TYR	ClinVar chrX:135738541 rs1603321148	Pathogenic/Likely pathogenic	-	0.694	Hyper-IgM syndrome type 1 [MONDO:MONDO:0010626,MedGen:C0398689,OMIM:308230,Orphanet:101088]
126_VAL	ALA	VAR_007515 -	LP/P	-	0.6207	Immunodeficiency with hyper-IgM, type 1 (HIGM1) [MIM:308230]
126_VAL	ASP	VAR_017931 -	LP/P	-	0.9703	Immunodeficiency with hyper-IgM, type 1 (HIGM1) [MIM:308230]
129_GLU	TER	ClinVar chrX:135738553 rs1215852570	Pathogenic	-	-	Hyper-IgM syndrome type 1 [MONDO:MONDO:0010626,MedGen:C0398689,OMIM:308230,Orphanet:101088]
138_LEU	SER	ClinVar chrX:135741201 -	Likely pathogenic	-	0.9619	not provided [MedGen:C3661900]
140_TRP	CYS	VAR_007517 -	LP/P	-	0.9961	Immunodeficiency with hyper-IgM, type 1 (HIGM1) [MIM:308230]
140_TRP	GLY	VAR_007518 rs104894777	LP/P	-	0.9212	Immunodeficiency with hyper-IgM, type 1 (HIGM1) [MIM:308230]
140_TRP	ARG	VAR_007519 -	LP/P	-	0.9955	Immunodeficiency with hyper-IgM, type 1 (HIGM1) [MIM:308230]
140_TRP	TER	ClinVar chrX:135741207 rs104894775	Pathogenic	-	-	Hyper-IgM syndrome type 1 [MONDO:MONDO:0010626,MedGen:C0398689,OMIM:308230,Orphanet:101088]
140_TRP	GLY	ClinVar chrX:135741206 rs104894777	Likely pathogenic	-	0.9212	Hyper-IgM syndrome type 1\|not provided [MONDO:MONDO:0010626,MedGen:C0398689,OMIM:308230,Orphanet:101088\|MedGen:C3661900]
140_TRP	ARG	ClinVar chrX:135741206 rs104894777	Pathogenic	-	0.9955	Hyper-IgM syndrome type 1 [MONDO:MONDO:0010626,MedGen:C0398689,OMIM:308230,Orphanet:101088]
140_TRP	CYS	ClinVar chrX:135741208 -	Pathogenic	-	0.9961	Hyper-IgM syndrome type 1 [MONDO:MONDO:0010626,MedGen:C0398689,OMIM:308230,Orphanet:101088]
141_ALA	PRO	ClinVar chrX:135741209 rs1387503550	Pathogenic	-	0.8444	Hyper-IgM syndrome type 1 [MONDO:MONDO:0010626,MedGen:C0398689,OMIM:308230,Orphanet:101088]
141_ALA	THR	8.3kJPN chrX:135741209 rs1387503550	-	0.0004	0.0894	-
143_LYS	THR	VAR_017932 -	LP/P	-	0.2596	Immunodeficiency with hyper-IgM, type 1 (HIGM1) [MIM:308230]
144_GLY	GLU	VAR_007520 rs886039326	LP/P	-	0.703	Immunodeficiency with hyper-IgM, type 1 (HIGM1) [MIM:308230]
144_GLY	GLU	ClinVar chrX:135741219 rs886039326	Likely pathogenic	-	0.703	not provided\|Hyper-IgM syndrome type 1 [MedGen:C3661900\|MONDO:MONDO:0010626,MedGen:C0398689,OMIM:308230,Orphanet:101088]
144_GLY	TER	ClinVar chrX:135741218 -	Likely pathogenic	-	-	not provided [MedGen:CN517202]
146_TYR	TER	ClinVar chrX:135741226 -	Pathogenic	-	-	Hyper-IgM syndrome type 1 [MONDO:MONDO:0010626,MedGen:C0398689,OMIM:308230,Orphanet:101088]
147_THR	ASN	VAR_017922 rs1057521127	LP/P	-	0.2723	Immunodeficiency with hyper-IgM, type 1 (HIGM1) [MIM:308230]
155_LEU	PRO	VAR_007521 rs104894769	LP/P	-	0.4622	Immunodeficiency with hyper-IgM, type 1 (HIGM1) [MIM:308230]
155_LEU	PRO	ClinVar chrX:135741252 rs104894769	Pathogenic	-	0.4622	Hyper-IgM syndrome type 1\|not provided [MONDO:MONDO:0010626,MedGen:C0398689,OMIM:308230,Orphanet:101088\|MedGen:C3661900]
155_LEU	GLN	ClinVar chrX:135741252 rs104894769	Likely pathogenic	-	0.2946	not provided [MedGen:CN517202]
160_GLN	TER	ClinVar chrX:135741266 rs767889061	Pathogenic	-	-	Hyper-IgM syndrome type 1 [MONDO:MONDO:0010626,MedGen:C0398689,OMIM:308230,Orphanet:101088]
163_VAL	ILE	gnomAD chrX:135741275 rs199914973	-	0.00013661	0.0794	-
167_GLY	ARG	ClinVar chrX:135741287 -	Pathogenic	-	0.9528	Hyper-IgM syndrome type 1 [MONDO:MONDO:0010626,MedGen:C0398689,OMIM:308230,Orphanet:101088]
169_TYR	CYS	ClinVar chrX:135741294 rs786205606	Likely pathogenic	-	0.8689	not provided [MedGen:C3661900]
170_TYR	CYS	VAR_017923 rs756468554	LP/P	-	0.7225	Immunodeficiency with hyper-IgM, type 1 (HIGM1) [MIM:308230]
170_TYR	TER	ClinVar chrX:135741298 -	Pathogenic	-	-	Hyper-IgM syndrome type 1 [MONDO:MONDO:0010626,MedGen:C0398689,OMIM:308230,Orphanet:101088]
170_TYR	CYS	ClinVar chrX:135741297 -	Likely pathogenic	-	0.7225	not provided [MedGen:CN517202]
172_TYR	HIS	ClinVar chrX:135741302 rs2076127133	Likely pathogenic	-	0.8067	Hyper-IgM syndrome type 1 [MONDO:MONDO:0010626,MedGen:C0398689,OMIM:308230,Orphanet:101088]
172_TYR	CYS	ClinVar chrX:135741303 -	Likely pathogenic	-	0.8096	Hyper-IgM syndrome type 1 [MONDO:MONDO:0010626,MedGen:C0398689,OMIM:308230,Orphanet:101088]
173_ALA	ASP	VAR_017933 -	LP/P	-	0.8992	Immunodeficiency with hyper-IgM, type 1 (HIGM1) [MIM:308230]
174_GLN	ARG	VAR_017927 -	LP/P	-	0.4477	Immunodeficiency with hyper-IgM, type 1 (HIGM1) [MIM:308230]
174_GLN	TER	ClinVar chrX:135741308 rs1603321772	Pathogenic	-	-	Hyper-IgM syndrome type 1 [MONDO:MONDO:0010626,MedGen:C0398689,OMIM:308230,Orphanet:101088]
176_THR	ILE	VAR_017934 -	LP/P	-	0.7515	Immunodeficiency with hyper-IgM, type 1 (HIGM1) [MIM:308230]
181_ARG	GLN	gnomAD chrX:135741330 rs11575982	-	0.00183427	0.0735	-
186_GLN	TER	ClinVar chrX:135741344 rs2076127276	Pathogenic	-	-	Hyper-IgM syndrome type 1 [MONDO:MONDO:0010626,MedGen:C0398689,OMIM:308230,Orphanet:101088]
195_LEU	PRO	VAR_017935 -	LP/P	-	0.9332	Immunodeficiency with hyper-IgM, type 1 (HIGM1) [MIM:308230]
199_GLY	SER	8.3kJPN chrX:135741383 rs769728462	-	0.0002	0.0691	-
200_ARG	TER	ClinVar chrX:135741386 rs2148553738	Pathogenic	-	-	Hyper-IgM syndrome type 1 [MONDO:MONDO:0010626,MedGen:C0398689,OMIM:308230,Orphanet:101088]
201_PHE	LEU	gnomAD chrX:135741389 rs144827029	-	0.000109186	0.29	-
202_GLU	GLN	8.3kJPN chrX:135741392 -	-	0.0001	0.1709	-
206_LEU	PRO	ClinVar chrX:135741405 -	Likely pathogenic	-	0.9752	not provided [MedGen:C3661900]
208_ALA	ASP	VAR_017936 -	LP/P	-	0.8616	Immunodeficiency with hyper-IgM, type 1 (HIGM1) [MIM:308230]
211_THR	ASN	VAR_007522 rs1569377829	LP/P	-	0.1442	Immunodeficiency with hyper-IgM, type 1 (HIGM1) [MIM:308230]
211_THR	ASN	ClinVar chrX:135741420 rs1569377829	Likely pathogenic	-	0.1442	Hyper-IgM syndrome type 1 [MONDO:MONDO:0010626,MedGen:C0398689,OMIM:308230,Orphanet:101088]
218_CYS	TER	ClinVar chrX:135741442 -	Pathogenic	-	-	Hyper-IgM syndrome type 1 [MONDO:MONDO:0010626,MedGen:C0398689,OMIM:308230,Orphanet:101088]
219_GLY	ARG	VAR_007523 rs148594123	LB/B	-	0.1015	-
219_GLY	ARG	gnomAD chrX:135741443 rs148594123	-	0.0110849	0.1015	-
220_GLN	TER	ClinVar chrX:135741446 rs1085307733	Pathogenic	-	-	not provided\|Hyper-IgM syndrome type 1 [MedGen:C3661900\|MONDO:MONDO:0010626,MedGen:C0398689,OMIM:308230,Orphanet:101088]
221_GLN	TER	ClinVar chrX:135741449 rs1603321834	Pathogenic	-	-	Hyper-IgM syndrome type 1 [MONDO:MONDO:0010626,MedGen:C0398689,OMIM:308230,Orphanet:101088]
224_HIS	TYR	VAR_017937 -	LP/P	-	0.1463	Immunodeficiency with hyper-IgM, type 1 (HIGM1) [MIM:308230]
225_LEU	SER	ClinVar chrX:135741462 rs2148553773	Likely pathogenic	-	0.7511	not provided [MedGen:C3661900]
226_GLY	ALA	VAR_017938 -	LP/P	-	0.4351	Immunodeficiency with hyper-IgM, type 1 (HIGM1) [MIM:308230]
227_GLY	VAL	VAR_007524 rs104894768	LP/P	-	0.8114	Immunodeficiency with hyper-IgM, type 1 (HIGM1) [MIM:308230]
227_GLY	VAL	ClinVar chrX:135741468 rs104894768	Pathogenic	-	0.8114	Hyper-IgM syndrome type 1 [MONDO:MONDO:0010626,MedGen:C0398689,OMIM:308230,Orphanet:101088]
229_PHE	LEU	ClinVar chrX:135741475 rs2148553785	Pathogenic	-	0.9787	not provided [MedGen:C3661900]
229_PHE	LEU	ClinVar chrX:135741475 -	Likely pathogenic	-	0.9787	Hyper-IgM syndrome type 1 [MONDO:MONDO:0010626,MedGen:C0398689,OMIM:308230,Orphanet:101088]
231_LEU	SER	VAR_007526 -	LP/P	-	0.9814	Immunodeficiency with hyper-IgM, type 1 (HIGM1) [MIM:308230]
232_GLN	TER	ClinVar chrX:135741482 rs2076127875	Pathogenic	-	-	Hyper-IgM syndrome type 1 [MONDO:MONDO:0010626,MedGen:C0398689,OMIM:308230,Orphanet:101088]
235_ALA	PRO	VAR_007527 rs104894771	LP/P	-	0.8072	Immunodeficiency with hyper-IgM, type 1 (HIGM1) [MIM:308230]
235_ALA	PRO	ClinVar chrX:135741491 rs104894771	Pathogenic	-	0.8072	Hyper-IgM syndrome type 1 [MONDO:MONDO:0010626,MedGen:C0398689,OMIM:308230,Orphanet:101088]
237_VAL	GLU	VAR_017939 -	LP/P	-	0.9563	Immunodeficiency with hyper-IgM, type 1 (HIGM1) [MIM:308230]
254_THR	MET	VAR_007528 rs193922136	LP/P	-	0.7653	Immunodeficiency with hyper-IgM, type 1 (HIGM1) [MIM:308230]
254_THR	MET	ClinVar chrX:135741549 rs193922136	Pathogenic	-	0.7653	Hyper-IgM syndrome type 1\|Hyperimmunoglobulin M syndrome [MONDO:MONDO:0010626,MedGen:C0398689,OMIM:308230,Orphanet:101088\|MONDO:MONDO:0003947,MedGen:C0272236,OMIM:PS308230]
254_THR	LYS	ClinVar chrX:135741549 rs193922136	Likely pathogenic	-	0.9708	Hyper-IgM syndrome type 1 [MONDO:MONDO:0010626,MedGen:C0398689,OMIM:308230,Orphanet:101088]
256_PHE	SER	ClinVar chrX:135741555 rs1057521128	Likely pathogenic	-	0.9626	not provided\|Hyper-IgM syndrome type 1 [MedGen:C3661900\|MONDO:MONDO:0010626,MedGen:C0398689,OMIM:308230,Orphanet:101088]
257_GLY	SER	VAR_017928 -	LP/P	-	0.8358	Immunodeficiency with hyper-IgM, type 1 (HIGM1) [MIM:308230]
257_GLY	ASP	VAR_017940 rs1477466218	LP/P	-	0.9869	Immunodeficiency with hyper-IgM, type 1 (HIGM1) [MIM:308230]
257_GLY	ASP	ClinVar chrX:135741558 rs1477466218	Pathogenic	-	0.9869	Hyper-IgM syndrome type 1 [MONDO:MONDO:0010626,MedGen:C0398689,OMIM:308230,Orphanet:101088]
257_GLY	VAL	ClinVar chrX:135741558 -	Likely pathogenic	-	0.9541	Hyper-IgM syndrome type 1 [MONDO:MONDO:0010626,MedGen:C0398689,OMIM:308230,Orphanet:101088]
258_LEU	SER	VAR_017924 rs1569377884	LP/P	-	0.9585	Immunodeficiency with hyper-IgM, type 1 (HIGM1) [MIM:308230]

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Reference

PiSite: a database of protein interaction sites using multiple binding states in the PDB, Miho Higurashi, Takashi Ishida and Kengo Kinoshita, Nucleic Acids Research 2009 37(Database issue):D360-D364

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Sequence information

Binding partner information

Binding partner information

Binding partner information

Binding partner information

Binding partner information

Binding partner information

Binding partner information

Variants

Reference

	P29965	CD40 ligand
	P29965	CD40 ligand
	P25942	Tumor necrosis factor receptor superfamily member 5

	P29965	CD40 ligand
	P29965	CD40 ligand
	P25942	Tumor necrosis factor receptor superfamily member 5
	P25942	Tumor necrosis factor receptor superfamily member 5

	P29965	CD40 ligand
	P29965	CD40 ligand
	7SGM	5c8* Fab light chain
	7SGM	5c8* Fab light chain
	7SGM	5c8* Fab heavy chain