2BC4 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HLA-DM

Authors :   M. J. Nicholson, B. Moradi, N. P. Seth, X. Xing, G. D. Cuny, R. L. Stein, K. W. Wucherpfennig

Date :   18 Oct 05 (Deposition) - 23 May 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.27

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)
Biol. Unit 3: A (1x),B (1x),C (1x),D (1x)

Keywords :   Mhc Class Ii, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. J. Nicholson, B. Moradi, N. P. Seth, X. Xing, G. D. Cuny, R. L. Stein, K. W. Wucherpfennig
Small Molecules That Enhance The Catalytic Efficiency Of Hla-Dm.
J. Immunol. V. 176 4208 2006
PubMed-ID: 16547258
(for further references see the PDB file header)

Molecule 1 - HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DM ALPHA CHAIN
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	DROSOPHILA MELANOGASTER
	Expression System Common	:	FRUIT FLY
	Expression System Plasmid	:	PRMHA-3
	Expression System Taxid	:	7227
	Expression System Vector Type	:	STABLE TRANSFECTION PLASMID
	Gene	:	HLA-DMA, DMA, RING6
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	MHC CLASS II ANTIGEN DMA

Molecule 2 - HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DM BETA CHAIN
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	DROSOPHILA MELANOGASTER
	Expression System Common	:	FRUIT FLY
	Expression System Plasmid	:	PRMHA-3
	Expression System Taxid	:	7227
	Expression System Vector Type	:	STABLE TRANSFECTION PLASMID
	Gene	:	HLA-DMB, DMB, RING7
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	MHC CLASS II ANTIGEN DMB

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (1x)	:	A (1x)	B (1x)	C (1x)	D (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 12)

No.	Name	Count	Type	Full Name
1	BMA	4	Ligand/Ion	BETA-D-MANNOSE
2	CL	4	Ligand/Ion	CHLORIDE ION
3	NDG	4	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	BMA	2	Ligand/Ion	BETA-D-MANNOSE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	NDG	2	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	BMA	2	Ligand/Ion	BETA-D-MANNOSE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	NDG	2	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

Biological Unit 3 (2, 4)

No.	Name	Count	Type	Full Name
1	BMA	2	Ligand/Ion	BETA-D-MANNOSE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	NDG	2	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LEU A:13 , ASN A:15 , NDG A:213 , HOH A:509 , HOH A:542 , LEU B:12 , LYS B:20 , VAL D:50	BINDING SITE FOR RESIDUE NDG A 212
02	AC2	SOFTWARE	NDG A:212 , BMA A:214 , LYS B:20	BINDING SITE FOR RESIDUE NDG A 213
03	AC3	SOFTWARE	NDG A:213 , BMA A:215 , ASN D:52	BINDING SITE FOR RESIDUE BMA A 214
04	AC4	SOFTWARE	ASP A:200 , BMA A:214	BINDING SITE FOR RESIDUE BMA A 215
05	AC5	SOFTWARE	GLY B:49 , VAL B:50 , ASP C:12 , LEU C:13 , ASN C:15 , NDG C:213 , HOH C:510 , HOH C:543 , HOH C:611 , LEU D:12 , LYS D:20 , GLY D:192 , PRO D:195	BINDING SITE FOR RESIDUE NDG C 212
06	AC6	SOFTWARE	PHE B:48 , GLY B:49 , VAL B:50 , NDG C:212 , BMA C:214 , LYS D:20 , TYR D:168 , GLY D:192 , LEU D:193	BINDING SITE FOR RESIDUE NDG C 213
07	AC7	SOFTWARE	ASN B:52 , SER B:53 , NDG C:213 , BMA C:215	BINDING SITE FOR RESIDUE BMA C 214
08	AC8	SOFTWARE	ASP C:200 , BMA C:214 , LEU D:193	BINDING SITE FOR RESIDUE BMA C 215
09	AC9	SOFTWARE	HIS B:145	BINDING SITE FOR RESIDUE CL B 501
10	BC1	SOFTWARE	ARG A:98	BINDING SITE FOR RESIDUE CL D 502
11	BC2	SOFTWARE	HOH C:542	BINDING SITE FOR RESIDUE CL C 504

Asymmetric Unit

No.	Residues
1	A:24	-	A:79
2	A:121	-	A:176
3	B:11	-	B:79
4	B:25	-	B:35
5	B:117	-	B:174
6	C:24	-	C:79
7	C:121	-	C:176
8	D:11	-	D:79
9	D:25	-	D:35
10	D:117	-	D:174

Asymmetric Unit

No.	Residues
1	Ser A:28	-	Pro A:29
2	Phe A:127	-	Pro A:128
3	Tyr B:123	-	Pro B:124
4	Ser C:28	-	Pro C:29
5	Phe C:127	-	Pro C:128
6	Tyr D:123	-	Pro D:124

Asymmetric Unit (13, 26)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_050360	T	28	A	DMB_HUMAN	Polymorphism	17583782	B/D	T	10	A
02	UniProt	VAR_016752	S	45	F	DMB_HUMAN	Polymorphism	41560814	B/D	S	27	F
03	UniProt	VAR_050361	D	49	V	DMB_HUMAN	Polymorphism	17617333	B/D	D	31	V
04	UniProt	VAR_050362	S	71	N	DMB_HUMAN	Polymorphism	17617321	B/D	S	53	N
05	UniProt	VAR_016746	H	162	Q	DMA_HUMAN	Polymorphism	---	A/C	Q	136	Q
06	UniProt	VAR_016747	D	163	H	DMA_HUMAN	Polymorphism	---	A/C	H	137	H
07	UniProt	VAR_016748	V	166	I	DMA_HUMAN	Polymorphism	1063478	A/C	V	140	I
08	UniProt	VAR_016753	A	162	E	DMB_HUMAN	Polymorphism	2071555	B/D	A	144	E
09	UniProt	VAR_016754	A	162	V	DMB_HUMAN	Polymorphism	2071555	B/D	A	144	V
10	UniProt	VAR_016749	G	181	A	DMA_HUMAN	Polymorphism	6926628	A/C	G	155	A
11	UniProt	VAR_016755	I	197	T	DMB_HUMAN	Polymorphism	1042337	B/D	I	179	T
12	UniProt	VAR_016750	R	210	C	DMA_HUMAN	Polymorphism	17214044	A/C	R	184	C
13	UniProt	VAR_016751	R	210	H	DMA_HUMAN	Polymorphism	41555121	A/C	R	184	H

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (13, 13)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_050360	T	28	A	DMB_HUMAN	Polymorphism	17583782	B	T	10	A
02	UniProt	VAR_016752	S	45	F	DMB_HUMAN	Polymorphism	41560814	B	S	27	F
03	UniProt	VAR_050361	D	49	V	DMB_HUMAN	Polymorphism	17617333	B	D	31	V
04	UniProt	VAR_050362	S	71	N	DMB_HUMAN	Polymorphism	17617321	B	S	53	N
05	UniProt	VAR_016746	H	162	Q	DMA_HUMAN	Polymorphism	---	A	Q	136	Q
06	UniProt	VAR_016747	D	163	H	DMA_HUMAN	Polymorphism	---	A	H	137	H
07	UniProt	VAR_016748	V	166	I	DMA_HUMAN	Polymorphism	1063478	A	V	140	I
08	UniProt	VAR_016753	A	162	E	DMB_HUMAN	Polymorphism	2071555	B	A	144	E
09	UniProt	VAR_016754	A	162	V	DMB_HUMAN	Polymorphism	2071555	B	A	144	V
10	UniProt	VAR_016749	G	181	A	DMA_HUMAN	Polymorphism	6926628	A	G	155	A
11	UniProt	VAR_016755	I	197	T	DMB_HUMAN	Polymorphism	1042337	B	I	179	T
12	UniProt	VAR_016750	R	210	C	DMA_HUMAN	Polymorphism	17214044	A	R	184	C
13	UniProt	VAR_016751	R	210	H	DMA_HUMAN	Polymorphism	41555121	A	R	184	H

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (13, 13)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_050360	T	28	A	DMB_HUMAN	Polymorphism	17583782	D	T	10	A
02	UniProt	VAR_016752	S	45	F	DMB_HUMAN	Polymorphism	41560814	D	S	27	F
03	UniProt	VAR_050361	D	49	V	DMB_HUMAN	Polymorphism	17617333	D	D	31	V
04	UniProt	VAR_050362	S	71	N	DMB_HUMAN	Polymorphism	17617321	D	S	53	N
05	UniProt	VAR_016746	H	162	Q	DMA_HUMAN	Polymorphism	---	C	Q	136	Q
06	UniProt	VAR_016747	D	163	H	DMA_HUMAN	Polymorphism	---	C	H	137	H
07	UniProt	VAR_016748	V	166	I	DMA_HUMAN	Polymorphism	1063478	C	V	140	I
08	UniProt	VAR_016753	A	162	E	DMB_HUMAN	Polymorphism	2071555	D	A	144	E
09	UniProt	VAR_016754	A	162	V	DMB_HUMAN	Polymorphism	2071555	D	A	144	V
10	UniProt	VAR_016749	G	181	A	DMA_HUMAN	Polymorphism	6926628	C	G	155	A
11	UniProt	VAR_016755	I	197	T	DMB_HUMAN	Polymorphism	1042337	D	I	179	T
12	UniProt	VAR_016750	R	210	C	DMA_HUMAN	Polymorphism	17214044	C	R	184	C
13	UniProt	VAR_016751	R	210	H	DMA_HUMAN	Polymorphism	41555121	C	R	184	H

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 3 (13, 26)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_050360	T	28	A	DMB_HUMAN	Polymorphism	17583782	B/D	T	10	A
02	UniProt	VAR_016752	S	45	F	DMB_HUMAN	Polymorphism	41560814	B/D	S	27	F
03	UniProt	VAR_050361	D	49	V	DMB_HUMAN	Polymorphism	17617333	B/D	D	31	V
04	UniProt	VAR_050362	S	71	N	DMB_HUMAN	Polymorphism	17617321	B/D	S	53	N
05	UniProt	VAR_016746	H	162	Q	DMA_HUMAN	Polymorphism	---	A/C	Q	136	Q
06	UniProt	VAR_016747	D	163	H	DMA_HUMAN	Polymorphism	---	A/C	H	137	H
07	UniProt	VAR_016748	V	166	I	DMA_HUMAN	Polymorphism	1063478	A/C	V	140	I
08	UniProt	VAR_016753	A	162	E	DMB_HUMAN	Polymorphism	2071555	B/D	A	144	E
09	UniProt	VAR_016754	A	162	V	DMB_HUMAN	Polymorphism	2071555	B/D	A	144	V
10	UniProt	VAR_016749	G	181	A	DMA_HUMAN	Polymorphism	6926628	A/C	G	155	A
11	UniProt	VAR_016755	I	197	T	DMB_HUMAN	Polymorphism	1042337	B/D	I	179	T
12	UniProt	VAR_016750	R	210	C	DMA_HUMAN	Polymorphism	17214044	A/C	R	184	C
13	UniProt	VAR_016751	R	210	H	DMA_HUMAN	Polymorphism	41555121	A/C	R	184	H

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	DMB_HUMAN	190-196	2	B:172-178 D:172-178
1	IG_MHC	PS00290		DMA_HUMAN	200-206	2	A:174-180 C:174-180

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	DMB_HUMAN	190-196	1	B:172-178 -
1	IG_MHC	PS00290		DMA_HUMAN	200-206	1	A:174-180 -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	DMB_HUMAN	190-196	1	- D:172-178
1	IG_MHC	PS00290		DMA_HUMAN	200-206	1	- C:174-180

Biological Unit 3 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	DMB_HUMAN	190-196	2	B:172-178 D:172-178
1	IG_MHC	PS00290		DMA_HUMAN	200-206	2	A:174-180 C:174-180

Asymmetric Unit (6, 12)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.12a	ENST00000383230	12a	ENSE00002182258	HSCHR6_MHC_SSTO:33010800-33010627	174	DMA_HUMAN	1-30	30	0	-	-
1.15a	ENST00000383230	15a	ENSE00001761558	HSCHR6_MHC_SSTO:33008481-33008197	285	DMA_HUMAN	30-125	96	2	A:13-99 C:12-99	87 88
1.15e	ENST00000383230	15e	ENSE00001659539	HSCHR6_MHC_SSTO:33007567-33007289	279	DMA_HUMAN	125-218	94	2	A:99-192 C:99-192	94 94
1.15j	ENST00000383230	15j	ENSE00002174862	HSCHR6_MHC_SSTO:33007077-33006949	129	DMA_HUMAN	218-261	44	2	A:192-200 C:192-206	9 15
1.16d	ENST00000383230	16d	ENSE00001818600	HSCHR6_MHC_SSTO:33006546-33006288	259	DMA_HUMAN	261-261	1	0	-	-

2.19a	ENST00000383231	19a	ENSE00001871999	HSCHR6_MHC_QBL:32837576-32837259	318	DMB_HUMAN	1-19	19	0	-	-
2.20a	ENST00000383231	20a	ENSE00001753767	HSCHR6_MHC_QBL:32835472-32835191	282	DMB_HUMAN	19-113	95	2	B:3-95 D:3-95	93 93
2.20e	ENST00000383231	20e	ENSE00002181255	HSCHR6_MHC_QBL:32833963-32833679	285	DMB_HUMAN	113-208	96	2	B:95-190 D:95-190	96 96
2.20i	ENST00000383231	20i	ENSE00001591922	HSCHR6_MHC_QBL:32832159-32832043	117	DMB_HUMAN	208-247	40	2	B:190-193 D:190-199	4 10
2.20k	ENST00000383231	20k	ENSE00001724215	HSCHR6_MHC_QBL:32831884-32831849	36	DMB_HUMAN	247-259	13	0	-	-
2.20n	ENST00000383231	20n	ENSE00001757202	HSCHR6_MHC_QBL:32831494-32831136	359	DMB_HUMAN	259-263	5	0	-	-

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:188
 aligned with DMA_HUMAN | P28067 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:188
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218        
            DMA_HUMAN    39 LQNHTFLHTVYCQDGSPSVGLSEAYDEDQLFFFDFSQNTRVPRLPEFADWAQEQGDAPAILFDKEFCEWMIQQIGPKLDGKIPVSRGFPIAEVFTLKPLEFGKPNTLVCFVSNLFPPMLTVNWHDHSVPVEGFGPTFVSAVDGLSFQAFSYLNFTPEPSDIFSCIVTHEIDRYTAIAYWVPRNALPSD 226
               SCOP domains d2bc4a1 A:13-96 automated matches                                                   d2bc4a2 A:97-200 automated matches                                                                       SCOP domains
               CATH domains 2bc4A01 A:13-91                                                                2bc4A02 A:92-200 Immunoglobulins                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee.....eeeeeee..eeeeeee....eeee.hhhhhhhhh...hhhhhhhhhhhhhhhhhh................eeeeee.........eeeeeeeeee....eeeeeee..eee......eeeee...eeeeeeeeee.......eeeeeee....eeeeeee......... Sec.struct. author
             SAPs(SNPs) (1) ---------------------------------------------------------------------------------------------------------------------------QH--I--------------A----------------------------C---------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------H---------------- SAPs(SNPs) (2)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC -------------------- PROSITE
           Transcript 1 (1) Exon 1.15a  PDB: A:13-99 UniProt: 30-125 [INCOMPLETE]                                  --------------------------------------------------------------------------------------------1.15j     Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------Exon 1.15e  PDB: A:99-192 UniProt: 125-218                                                    -------- Transcript 1 (2)
                 2bc4 A  13 LQNHTFLHTVYCQDGSPSVGLSEAYDEDQLFFFDFSQNTRVPRLPEFADWAQEQGDAPAILFDKEFCEWMIQQIGPKLDGKIPVSRGFPIAEVFTLKPLEFGKPNTLVCFVSNLFPPMLTVNWQHHSVPVEGFGPTFVSAVDGLSFQAFSYLNFTPEPSDIFSCIVTHEIDRYTAIAYWVPRNALPSD 200
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192

Chain B from PDB  Type:PROTEIN  Length:191
 aligned with DMB_HUMAN | P28068 from UniProtKB/Swiss-Prot  Length:263

    Alignment length:191
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210 
            DMB_HUMAN    21 FVAHVESTCLLDDAGTPKDFTYCISFNKDLLTCWDPEENKMAPCEFGVLNSLANVLSQHLNQKDTLMQRLRNGLQNCATHTQPFWGSLTNRTRPPSVQVAKTTPFNTREPVMLACYVWGFYPAEVTITWRKNGKLVMPHSSAHKTAQPNGDWTYQTLSHLALTPSYGDTYTCVVEHIGAPEPILRDWTPGL 211
               SCOP domains d2bc4b1 B:3-93 automated matches                                                           d2bc4b2 B:94-193 automated matches                                                                   SCOP domains
               CATH domains 2bc4B01 B:3-92 Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1       2bc4B02 B:93-193 Immunoglobulins                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee....eeeeeeeeee..eeeeeee....eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.........eeeeeeeeee.....eeeeee..eee..........ee.....eeeeeeeee.......eeeeee.......eeeee.... Sec.struct. author
             SAPs(SNPs) (1) -------A----------------F---V---------------------N------------------------------------------------------------------------------------------E----------------------------------T-------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ---------------------------------------------------------------------------------------------------------------------------------------------V------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC --------------- PROSITE
           Transcript 2 (1) Exon 2.20a  PDB: B:3-95 UniProt: 19-113 [INCOMPLETE]                                         ----------------------------------------------------------------------------------------------2.20 Transcript 2 (1)
           Transcript 2 (2) --------------------------------------------------------------------------------------------Exon 2.20e  PDB: B:95-190 UniProt: 113-208                                                      --- Transcript 2 (2)
                 2bc4 B   3 FVAHVESTCLLDDAGTPKDFTYCISFNKDLLTCWDPEENKMAPCEFGVLNSLANVLSQHLNQKDTLMQRLRNGLQNCATHTQPFWGSLTNRTRPPSVQVAKTTPFNTREPVMLACYVWGFYPAEVTITWRKNGKLVMPHSSAHKTAQPNGDWTYQTLSHLALTPSYGDTYTCVVEHIGAPEPILRDWTPGL 193
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192

Chain C from PDB  Type:PROTEIN  Length:195
 aligned with DMA_HUMAN | P28067 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:195
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227     
            DMA_HUMAN    38 DLQNHTFLHTVYCQDGSPSVGLSEAYDEDQLFFFDFSQNTRVPRLPEFADWAQEQGDAPAILFDKEFCEWMIQQIGPKLDGKIPVSRGFPIAEVFTLKPLEFGKPNTLVCFVSNLFPPMLTVNWHDHSVPVEGFGPTFVSAVDGLSFQAFSYLNFTPEPSDIFSCIVTHEIDRYTAIAYWVPRNALPSDLLENVL 232
               SCOP domains d2bc4c1 C:12-96 automated matches                                                    d2bc4c2 C:97-206 automated matches                                                                             SCOP domains
               CATH domains 2bc4C01 C:12-91                                                                 2bc4C02 C:92-206 Immunoglobulins                                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeee.....eeeeeee..eeeeeee....eeee.hhhhhhhhh...hhhhhhhhhhhhhhhhhhh...............eeeeee.........eeeeeeeeee....eeeeeee..eee..eeeeeeeee...eeeeeeeeee.......eeeeeee....eeeeeee.......ee.hhhhh Sec.struct. author
             SAPs(SNPs) (1) ----------------------------------------------------------------------------------------------------------------------------QH--I--------------A----------------------------C---------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------H---------------------- SAPs(SNPs) (2)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC -------------------------- PROSITE
           Transcript 1 (1) Exon 1.15a  PDB: C:12-99 UniProt: 30-125 [INCOMPLETE]                                   --------------------------------------------------------------------------------------------Exon 1.15j      Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------Exon 1.15e  PDB: C:99-192 UniProt: 125-218                                                    -------------- Transcript 1 (2)
                 2bc4 C  12 DLQNHTFLHTVYCQDGSPSVGLSEAYDEDQLFFFDFSQNTRVPRLPEFADWAQEQGDAPAILFDKEFCEWMIQQIGPKLDGKIPVSRGFPIAEVFTLKPLEFGKPNTLVCFVSNLFPPMLTVNWQHHSVPVEGFGPTFVSAVDGLSFQAFSYLNFTPEPSDIFSCIVTHEIDRYTAIAYWVPRNALPSDLLEDYK 206
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201

Chain D from PDB  Type:PROTEIN  Length:197
 aligned with DMB_HUMAN | P28068 from UniProtKB/Swiss-Prot  Length:263

    Alignment length:197
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       
            DMB_HUMAN    21 FVAHVESTCLLDDAGTPKDFTYCISFNKDLLTCWDPEENKMAPCEFGVLNSLANVLSQHLNQKDTLMQRLRNGLQNCATHTQPFWGSLTNRTRPPSVQVAKTTPFNTREPVMLACYVWGFYPAEVTITWRKNGKLVMPHSSAHKTAQPNGDWTYQTLSHLALTPSYGDTYTCVVEHIGAPEPILRDWTPGLSPMQTL 217
               SCOP domains d2bc4d1 D:3-93 automated matches                                                           d2bc4d2 D:94-199 automated matches                                                                         SCOP domains
               CATH domains 2bc4D01 D:3-92 Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1       2bc4D02 D:93-199 Immunoglobulins                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee....eeeeeeeeee..eeeeee.hhhh.eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.........eeeeeeeeee.....eeeeee...ee..........ee.....eeeeeeeee.......eeeeee.......eeeee...hhh.ee. Sec.struct. author
             SAPs(SNPs) (1) -------A----------------F---V---------------------N------------------------------------------------------------------------------------------E----------------------------------T-------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ---------------------------------------------------------------------------------------------------------------------------------------------V------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC --------------------- PROSITE
           Transcript 2 (1) Exon 2.20a  PDB: D:3-95 UniProt: 19-113 [INCOMPLETE]                                         ----------------------------------------------------------------------------------------------Exon 2.20i Transcript 2 (1)
           Transcript 2 (2) --------------------------------------------------------------------------------------------Exon 2.20e  PDB: D:95-190 UniProt: 113-208                                                      --------- Transcript 2 (2)
                 2bc4 D   3 FVAHVESTCLLDDAGTPKDFTYCISFNKDLLTCWDPEENKMAPCEFGVLNSLANVLSQHLNQKDTLMQRLRNGLQNCATHTQPFWGSLTNRTRPPSVQVAKTTPFNTREPVMLACYVWGFYPAEVTITWRKNGKLVMPHSSAHKTAQPNGDWTYQTLSHLALTPSYGDTYTCVVEHIGAPEPILRDWTPGLSPMQTL 199
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Immunoglobulin (5995)

Family: C1 set domains (antibody constant domain-like) (3013)

Protein domain: automated matches (652)

Human (Homo sapiens) [TaxId: 9606] (334)

1a	d2bc4a2	A:97-200
1b	d2bc4b2	B:94-193
1c	d2bc4c2	C:97-206
1d	d2bc4d2	D:94-199

Class: Alpha and beta proteins (a+b) (23004)

Fold: MHC antigen-recognition domain (585)

Superfamily: MHC antigen-recognition domain (585)

Family: MHC antigen-recognition domain (533)

Protein domain: automated matches (29)

Human (Homo sapiens) [TaxId: 9606] (24)

2a	d2bc4a1	A:13-96
2b	d2bc4b1	B:3-93
2c	d2bc4c1	C:12-96
2d	d2bc4d1	D:3-93

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 (75)

Homologous Superfamily: Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 (75)

Human (Homo sapiens) (48)

1a	2bc4B01	B:3-92
1b	2bc4D01	D:3-92
1c	2bc4C01	C:12-91
1d	2bc4A01	A:13-91

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Human (Homo sapiens) (912)

2a	2bc4D02	D:93-199
2b	2bc4B02	B:93-193
2c	2bc4A02	A:92-200
2d	2bc4C02	C:92-206

(no "Pfam Domain" information available for 2BC4)

Asymmetric Unit(hide GO term definitions)

Chain A,C (DMA_HUMAN | P28067)

molecular function
	GO:0023026	MHC class II protein complex binding	Interacting selectively and non-covalently with the class II major histocompatibility complex.
biological process
	GO:0019882	antigen processing and presentation	The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex.
	GO:0019886	antigen processing and presentation of exogenous peptide antigen via MHC class II	The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class II protein complex. The peptide antigen is typically, but not always, processed from a whole protein.
	GO:0002504	antigen processing and presentation of peptide or polysaccharide antigen via MHC class II	The process in which an antigen-presenting cell expresses antigen (peptide or polysaccharide) on its cell surface in association with an MHC class II protein complex.
	GO:0006955	immune response	Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
	GO:0002376	immune system process	Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
	GO:0002503	peptide antigen assembly with MHC class II protein complex	The binding of a peptide to the antigen binding groove of an MHC class II protein complex.
cellular component
	GO:0042613	MHC class II protein complex	A transmembrane protein complex composed of an MHC class II alpha and MHC class II beta chain, and with or without a bound peptide or polysaccharide antigen.
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0031902	late endosome membrane	The lipid bilayer surrounding a late endosome.
	GO:0005765	lysosomal membrane	The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm.
	GO:0005764	lysosome	A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain B,D (DMB_HUMAN | P28068)

molecular function
	GO:0023026	MHC class II protein complex binding	Interacting selectively and non-covalently with the class II major histocompatibility complex.
biological process
	GO:0002399	MHC class II protein complex assembly	The aggregation, arrangement and bonding together of a set of components to form an MHC class II protein complex.
	GO:0019882	antigen processing and presentation	The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex.
	GO:0019886	antigen processing and presentation of exogenous peptide antigen via MHC class II	The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class II protein complex. The peptide antigen is typically, but not always, processed from a whole protein.
	GO:0002504	antigen processing and presentation of peptide or polysaccharide antigen via MHC class II	The process in which an antigen-presenting cell expresses antigen (peptide or polysaccharide) on its cell surface in association with an MHC class II protein complex.
	GO:0006955	immune response	Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
	GO:0002376	immune system process	Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
	GO:0002503	peptide antigen assembly with MHC class II protein complex	The binding of a peptide to the antigen binding groove of an MHC class II protein complex.
	GO:2001190	positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell	Any process that activates or increases the frequency, rate or extent of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell.
	GO:0042102	positive regulation of T cell proliferation	Any process that activates or increases the rate or extent of T cell proliferation.
cellular component
	GO:0042613	MHC class II protein complex	A transmembrane protein complex composed of an MHC class II alpha and MHC class II beta chain, and with or without a bound peptide or polysaccharide antigen.
	GO:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0031902	late endosome membrane	The lipid bilayer surrounding a late endosome.
	GO:0005765	lysosomal membrane	The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm.
	GO:0005764	lysosome	A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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	2bc4
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	DMA_HUMAN \| P28067
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	DMA_HUMAN \| P28067	:	1hdm 4fqx 4gbx
	DMB_HUMAN \| P28068	:	1hdm 4fqx 4gbx 4i0p

(no "Related Entries Specified in the PDB File" available for 2BC4)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 12)

Sites (11, 11)

SS Bonds (10, 10)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (13, 26)

PROSITE Motifs (1, 4)

Exons (6, 12)

Sequences/Alignments

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SCOP Domains (2, 8)

CATH Domains (2, 8)

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