1D9K - 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)

Biological Unit 4 (Jmol Viewer)

Biological Unit 5 (Jmol Viewer)

Biological Unit 6 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF COMPLEX BETWEEN D10 TCR AND PMHC I-AK/CA

Authors :   E. L. Reinherz, K. Tan, L. Tang, P. Kern, J. -H. Liu, Y. Xiong, R. E. Hussey A. Smolyar, B. Hare, R. Zhang, A. Joachimiak, H. -C. Chang, G. Wagner, J

Date :   28 Oct 99 (Deposition) - 15 Dec 99 (Release) - 01 Feb 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.20

Chains :   Asym. Unit : A,B,C,D,E,F,G,H,P,Q
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D,P  (1x)
Biol. Unit 3: E,F  (1x)
Biol. Unit 4: G,H,Q  (1x)
Biol. Unit 5: E,F,G,H,Q  (1x)
Biol. Unit 6: A,B,C,D,P  (1x)

Keywords :   T-Cell Receptor, Mhc Class Ii, D10, I-Ak, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. L. Reinherz, K. Tan, L. Tang, P. Kern, J. Liu, Y. Xiong, R. E. Hussey, A. Smolyar, B. Hare, R. Zhang, A. Joachimiak, H. C. Chang, G. Wagner, J. Wang
The Crystal Structure Of A T Cell Receptor In Complex With Peptide And Mhc Class Ii.
Science V. 286 1913 1999
PubMed-ID: 10583947 | Reference-DOI: 10.1126/SCIENCE.286.5446.1913

Molecule 1 - T-CELL RECEPTOR D10 (ALPHA CHAIN)
	Chains	:	A, E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-11A
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 2 - T-CELL RECEPTOR D10 (BETA CHAIN)
	Chains	:	B, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-11A
	Expression System Taxid	:	562
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 3 - MHC I-AK A CHAIN (ALPHA CHAIN)
	Chains	:	C, G
	Engineered	:	YES
	Expression System	:	CRICETULUS GRISEUS
	Expression System Common	:	CHINESE HAMSTER
	Expression System Plasmid	:	PEE14
	Expression System Taxid	:	10029
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	MHC I-AK

Molecule 4 - MHC I-AK B CHAIN (BETA CHAIN)
	Chains	:	D, H
	Engineered	:	YES
	Expression System	:	CRICETULUS GRISEUS
	Expression System Common	:	CHINESE HAMSTER
	Expression System Plasmid	:	PEE14
	Expression System Taxid	:	10029
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	MHC I-AK

Molecule 5 - CONALBUMIN PEPTIDE
	Chains	:	P, Q
	Engineered	:	YES
	Expression System	:	CRICETULUS GRISEUS
	Expression System Common	:	CHINESE HAMSTER
	Expression System Plasmid	:	PEE14
	Expression System Taxid	:	10029
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

		1	2	3	4	5	6	7	8	9	10
Asymmetric Unit	:	A	B	C	D	E	F	G	H	P	Q
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D					P
Biological Unit 3 (1x)	:					E	F
Biological Unit 4 (1x)	:							G	H		Q
Biological Unit 5 (1x)	:					E	F	G	H		Q
Biological Unit 6 (1x)	:	A	B	C	D					P

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 10)

No.	Name	Count	Type	Full Name
1	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	NDG	9	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	NAG	-1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	NDG	-1	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

Biological Unit 2 (1, 5)

No.	Name	Count	Type	Full Name
1	NAG	-1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	NDG	5	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	NAG	-1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	NDG	-1	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

Biological Unit 4 (2, 5)

No.	Name	Count	Type	Full Name
1	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	NDG	4	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

Biological Unit 5 (2, 5)

No.	Name	Count	Type	Full Name
1	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	NDG	4	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

Biological Unit 6 (1, 5)

No.	Name	Count	Type	Full Name
1	NAG	-1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	NDG	5	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LYS C:75 , ASN C:78	BINDING SITE FOR RESIDUE NDG C 201
02	AC2	SOFTWARE	ASN C:118 , LYS C:164 , GLU C:166 , NDG C:212	BINDING SITE FOR RESIDUE NDG C 211
03	AC3	SOFTWARE	NDG C:211	BINDING SITE FOR RESIDUE NDG C 212
04	AC4	SOFTWARE	ASN D:19 , GLN D:22 , NDG D:202	BINDING SITE FOR RESIDUE NDG D 201
05	AC5	SOFTWARE	NDG D:201	BINDING SITE FOR RESIDUE NDG D 202
06	AC6	SOFTWARE	ASN G:78	BINDING SITE FOR RESIDUE NDG G 201
07	AC7	SOFTWARE	ASN G:118 , TRP G:168 , NDG G:212	BINDING SITE FOR RESIDUE NDG G 211
08	AC8	SOFTWARE	NDG G:211	BINDING SITE FOR RESIDUE NDG G 212
09	AC9	SOFTWARE	ASN H:19 , GLN H:22 , NDG H:202	BINDING SITE FOR RESIDUE NAG H 201
10	BC1	SOFTWARE	NAG H:201	BINDING SITE FOR RESIDUE NDG H 202

Asymmetric Unit

No.	Residues
1	A:22	-	A:90
2	B:23	-	B:92
3	C:107	-	C:163
4	D:15	-	D:79
5	D:117	-	D:173
6	E:22	-	E:90
7	F:23	-	F:92
8	G:107	-	G:163
9	H:15	-	H:79
10	H:117	-	H:173

Asymmetric Unit

No.	Residues
1	Ser C:15	-	Pro C:16
2	Phe C:113	-	Pro C:114
3	Tyr D:123	-	Pro D:124
4	Ser G:15	-	Pro G:16
5	Phe G:113	-	Pro G:114
6	Tyr H:123	-	Pro H:124

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_TRFE_CHICK_003 *	R	154	W	TRFE_CHICK	---	---	P/Q	R	135	W
	* ID not provided by source

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

Biological Unit 1 (0, 0)

						dbSNP	PDB
No.	Source	Variant ID	Variant	UniProt ID	Status	ID	Chain	Variant

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

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_TRFE_CHICK_003 *	R	154	W	TRFE_CHICK	---	---	P	R	135	W
	* ID not provided by source

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

Biological Unit 3 (0, 0)

						dbSNP	PDB
No.	Source	Variant ID	Variant	UniProt ID	Status	ID	Chain	Variant

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

Biological Unit 4 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_TRFE_CHICK_003 *	R	154	W	TRFE_CHICK	---	---	Q	R	135	W
	* ID not provided by source

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

Biological Unit 5 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_TRFE_CHICK_003 *	R	154	W	TRFE_CHICK	---	---	Q	R	135	W
	* ID not provided by source

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

Biological Unit 6 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_TRFE_CHICK_003 *	R	154	W	TRFE_CHICK	---	---	P	R	135	W
	* ID not provided by source

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.	HA2K_MOUSE	188-194	2	C:161-167 G:161-167
1	IG_MHC	PS00290		HB2K_MOUSE	197-203	2	D:171-177 H:171-177

Biological Unit 1 (, 0)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	HA2K_MOUSE	188-194	0	- -
1	IG_MHC	PS00290		HB2K_MOUSE	197-203	0	- -

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.	HA2K_MOUSE	188-194	1	C:161-167 -
1	IG_MHC	PS00290		HB2K_MOUSE	197-203	1	D:171-177 -

Biological Unit 3 (, 0)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	HA2K_MOUSE	188-194	0	- -
1	IG_MHC	PS00290		HB2K_MOUSE	197-203	0	- -

Biological Unit 4 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	HA2K_MOUSE	188-194	1	- G:161-167
1	IG_MHC	PS00290		HB2K_MOUSE	197-203	1	- H:171-177

Biological Unit 5 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	HA2K_MOUSE	188-194	1	- G:161-167
1	IG_MHC	PS00290		HB2K_MOUSE	197-203	1	- H:171-177

Biological Unit 6 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	HA2K_MOUSE	188-194	1	C:161-167 -
1	IG_MHC	PS00290		HB2K_MOUSE	197-203	1	D:171-177 -

(no "Exon" information available for 1D9K)

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
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:110
                                                                                                                                               
               SCOP domains d1d9ka_ A: T-cell antigen receptor                                                                             SCOP domains
               CATH domains 1d9kA00 A:2-117 Immunoglobulins                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.....eeee....eeeeeee.........eee.......ee.........eeee..eeeeee....eeeeee...........eeee.......ee.....eeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                1d9k A    2 QVRQSPQSLTVWEGETTILNCSYEDSTFDYFPWYRQFPGKSPALLIAISLVSNKKEDGRFTIFFNKREKKLSLHITDSQPGDSATYFCAATGSFNKLTFGAGTRLAVSPY  117
                                    11        21        31        41        51       |62        72        82        92||     107       117
                                                                                    59|                              93|                  
                                                                                     61                               99

Chain B from PDB  Type:PROTEIN  Length:112
 aligned with TVB5_MOUSE | P04213 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:114
                                                                                                                                         122  
                                    20        30        40        50        60        70        80        90       100       110       120 |  
          TVB5_MOUSE     11 AVTQSPRSKVAVTGGKVTLSCHQTNNHDYMYWYRQDTGHGLRLIHYSYVADSTEKGDIPDGYKASRPSQENFSLILELASLSQTAVYFCASSGTGGALDTQYFGPGTRLLVL--    -
               SCOP domains d1d9kb_ B: T-cell antigen receptor                                                                                 SCOP domains
               CATH domains 1d9kB00 B:3-116C Immunoglobulins                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee....eeee.....eeeeeee.........eee...........................eeeeee..eeeeee...hhhhh.eee.ee..hhh--hh.ee...eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                1d9k B    3 AVTQSPRNKVAVTGGKVTLSCNQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGDIPDGYKASRPSQENFSLILELATPSQTSVYFCASGGQGR--AEQFFGPGTRLTVLGS 116C
                                    12        22        32        42        52        62||      73        83        93     | 105       115 |||
                                                                                       63|                                99  |         116A||
                                                                                        65                                  104          116B|
                                                                                                                                          116C

Chain C from PDB  Type:PROTEIN  Length:183
 aligned with HA2K_MOUSE | P01910 from UniProtKB/Swiss-Prot  Length:256

    Alignment length:183
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206   
          HA2K_MOUSE     27 IEADHVGSYGITVYQSPGDIGQYTFEFDGDELFYVDLDKKETVWMLPEFAQLRRFEPQGGLQNIATGKHNLEILTKRSNSTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVINITWLRNSKSVTDGVYETSFFVNRDYSFHKLSYLTFIPSDDDIYDCKVEHWGLEEPVLKHWEPEI  209
               SCOP domains d1d9kc2 C:1-81 Class II MHC alpha chain, N-terminal domain                        d1d9kc1 C:82-182 Class II MHC alpha chain, C-terminal domain                                          SCOP domains
               CATH domains --1d9kC01 C:3-81                                                                  1d9kC02 C:82-181 Immunoglobulins                                                                    - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeeee...eeeeeeee..eeeeeee....eeee...hhhhhheehhhhhhhhhhhhhhhhhhhhhhh.............eee.........eeeeeeeeee.....eeeeee...ee...eee...ee.....eeeeeeeee.......eeeeee.......eeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC --------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1d9k C    1 IEADHVGSYGITVYQSPGDIGQYTFEFDGDELFYVDLDKKETVWMLPEFAQLRRFEPQGGLQNIATGKHNLEILTKRSNSTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVINITWLRNSKSVTDGVYETSFFVNRDYSFHKLSYLTFIPSDDDIYDCKVEHWGLEEPVLKHWEPEI  182
                                    9A        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179   
                                    9A

Chain D from PDB  Type:PROTEIN  Length:188
 aligned with HB2K_MOUSE | P06343 from UniProtKB/Swiss-Prot  Length:263

    Alignment length:188
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208        
          HB2K_MOUSE     29 NSERHFVHQFQPFCYFTNGTQRIRLVIRYIYNREEYVRFDSDVGEYRAVTELGRPDAEYWNKQYLERTRAELDTVCRHNYEKTETPTSLRRLEQPSVVISLSRTEALNHHNTLVCSVTDFYPAKIKVRWFRNGQEETVGVSSTQLIRNGDWTFQVLVMLEMTPRRGEVYTCHVEHPSLKSPITVEWRA  216
               SCOP domains d1d9kd2 D:2-92 Class II MHC beta chain, N-terminal domain                                 d1d9kd1 D:93-190 Class II MHC beta chain, C-terminal domain                                        SCOP domains
               CATH domains 1d9kD01 D:2-92 Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1       1d9kD02 D:93-190 Immunoglobulins                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeeeehhhheeeeeeeeee..eeeeeee.....ee..hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh............ee.............eeee..eeee.....eeeeee..eee.........ee.....eee..eeee.......eeeeee.......eeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1d9k D    2 GSERHFVHQFQPFCYFTNGTQRIRLVIRYIYNREEYVRFDSDVGEYRAVTELGRPDAEYWNKQYLERTRAELDTVCRHNYEKTETPTSLRRLEQPSVVISLSRTEALNHHNTLVCSVTDFYPAKIKVRWFRNGQEETVGVSSTQLIRNGDWTFQVLVMLEMTPRRGEVYTCHVEHPSLKSPITVEWRA  190
                                    11        21        31        41        51        61  ||    73        83 |      92       102       112       122       132       142       152       162       172       182        
                                                                                         64|               84A                                                                                                          
                                                                                          67

Chain E from PDB  Type:PROTEIN  Length:110
                                                                                                                                               
               SCOP domains d1d9ke_ E: T-cell antigen receptor                                                                             SCOP domains
               CATH domains 1d9kE00 E:2-117 Immunoglobulins                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee....eeee....eeeeeee......eeeeeee.....eeeeeeee....eeee..eeeeee....eeeeee........eeeeeee.......ee...eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                1d9k E    2 QVRQSPQSLTVWEGETTILNCSYEDSTFDYFPWYRQFPGKSPALLIAISLVSNKKEDGRFTIFFNKREKKLSLHITDSQPGDSATYFCAATGSFNKLTFGAGTRLAVSPY  117
                                    11        21        31        41        51       |62        72        82        92||     107       117
                                                                                    59|                              93|                  
                                                                                     61                               99

Chain F from PDB  Type:PROTEIN  Length:112
 aligned with TVB5_MOUSE | P04213 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:114
                                                                                                                                         122  
                                    20        30        40        50        60        70        80        90       100       110       120 |  
          TVB5_MOUSE     11 AVTQSPRSKVAVTGGKVTLSCHQTNNHDYMYWYRQDTGHGLRLIHYSYVADSTEKGDIPDGYKASRPSQENFSLILELASLSQTAVYFCASSGTGGALDTQYFGPGTRLLVL--    -
               SCOP domains d1d9kf_ F: T-cell antigen receptor                                                                                 SCOP domains
               CATH domains 1d9kF00 F:3-116C Immunoglobulins                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee...eeee......eeeeee.....eeee............eee......ee.......eeeeee..eeeee....hhhhh.ee.eeee....--...ee...eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                1d9k F    3 AVTQSPRNKVAVTGGKVTLSCNQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGDIPDGYKASRPSQENFSLILELATPSQTSVYFCASGGQGR--AEQFFGPGTRLTVLGS 116C
                                    12        22        32        42        52        62||      73        83        93     | 105       115 |||
                                                                                       63|                                99  |         116A||
                                                                                        65                                  104          116B|
                                                                                                                                          116C

Chain G from PDB  Type:PROTEIN  Length:183
 aligned with HA2K_MOUSE | P01910 from UniProtKB/Swiss-Prot  Length:256

    Alignment length:183
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206   
          HA2K_MOUSE     27 IEADHVGSYGITVYQSPGDIGQYTFEFDGDELFYVDLDKKETVWMLPEFAQLRRFEPQGGLQNIATGKHNLEILTKRSNSTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVINITWLRNSKSVTDGVYETSFFVNRDYSFHKLSYLTFIPSDDDIYDCKVEHWGLEEPVLKHWEPEI  209
               SCOP domains d1d9kg2 G:1-81 Class II MHC alpha chain, N-terminal domain                        d1d9kg1 G:82-182 Class II MHC alpha chain, C-terminal domain                                          SCOP domains
               CATH domains --1d9kG01 G:3-81                                                                  1d9kG02 G:82-181 Immunoglobulins                                                                    - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee...eeee...eee.eeee..eeeeee......eee.hhhhh...ee.hhhhhhhhhhhhhhhhhhhhhh.............eee.........eeeee.eeee.......eee.........eee...ee.....eee.eeeee.......eeee...........eee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC --------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1d9k G    1 IEADHVGSYGITVYQSPGDIGQYTFEFDGDELFYVDLDKKETVWMLPEFAQLRRFEPQGGLQNIATGKHNLEILTKRSNSTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVINITWLRNSKSVTDGVYETSFFVNRDYSFHKLSYLTFIPSDDDIYDCKVEHWGLEEPVLKHWEPEI  182
                                    9A        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179   
                                    9A

Chain H from PDB  Type:PROTEIN  Length:188
 aligned with HB2K_MOUSE | P06343 from UniProtKB/Swiss-Prot  Length:263

    Alignment length:188
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208        
          HB2K_MOUSE     29 NSERHFVHQFQPFCYFTNGTQRIRLVIRYIYNREEYVRFDSDVGEYRAVTELGRPDAEYWNKQYLERTRAELDTVCRHNYEKTETPTSLRRLEQPSVVISLSRTEALNHHNTLVCSVTDFYPAKIKVRWFRNGQEETVGVSSTQLIRNGDWTFQVLVMLEMTPRRGEVYTCHVEHPSLKSPITVEWRA  216
               SCOP domains d1d9kh2 H:2-92 Class II MHC beta chain, N-terminal domain                                 d1d9kh1 H:93-190 Class II MHC beta chain, C-terminal domain                                        SCOP domains
               CATH domains 1d9kH01 H:2-92 Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1       1d9kH02 H:93-190 Immunoglobulins                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeee.hhhh.eeeeeeeee..eeeeeee....eee.....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh............ee..ee.........eeee..ee.......eeeee.........eee...ee.....ee..eeeee........eeeee.......eeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1d9k H    2 GSERHFVHQFQPFCYFTNGTQRIRLVIRYIYNREEYVRFDSDVGEYRAVTELGRPDAEYWNKQYLERTRAELDTVCRHNYEKTETPTSLRRLEQPSVVISLSRTEALNHHNTLVCSVTDFYPAKIKVRWFRNGQEETVGVSSTQLIRNGDWTFQVLVMLEMTPRRGEVYTCHVEHPSLKSPITVEWRA  190
                                    11        21        31        41        51        61  ||    73        83 |      92       102       112       122       132       142       152       162       172       182        
                                                                                         64|               84A                                                                                                          
                                                                                          67

Chain P from PDB  Type:PROTEIN  Length:16
 aligned with TRFE_CHICK | P02789 from UniProtKB/Swiss-Prot  Length:705

    Alignment length:27
                                   148       158       
          TRFE_CHICK    139 GRSAGWNIPIGTLLHRGAIEWEGIESG  165
               SCOP domains --------------------------- SCOP domains
               CATH domains --------------------------- CATH domains
               Pfam domains --------------------------- Pfam domains
         Sec.struct. author ..e-----------e............ Sec.struct. author
                 SAPs(SNPs) ---------------W----------- SAPs(SNPs)
                    PROSITE --------------------------- PROSITE
                 Transcript --------------------------- Transcript
                1d9k P  131 GNS-----------HRGAIEWEGIESG  146
                              |      -    |  139       
                            133         134

Chain Q from PDB  Type:PROTEIN  Length:16
 aligned with TRFE_CHICK | P02789 from UniProtKB/Swiss-Prot  Length:705

    Alignment length:27
                                   148       158       
          TRFE_CHICK    139 GRSAGWNIPIGTLLHRGAIEWEGIESG  165
               SCOP domains --------------------------- SCOP domains
               CATH domains --------------------------- CATH domains
               Pfam domains --------------------------- Pfam domains
         Sec.struct. author ..e-----------e............ Sec.struct. author
                 SAPs(SNPs) ---------------W----------- SAPs(SNPs)
                    PROSITE --------------------------- PROSITE
                 Transcript --------------------------- Transcript
                1d9k Q  131 GNS-----------HRGAIEWEGIESG  146
                              |      -    |  139       
                            133         134

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(

)

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)

House mouse (Mus musculus) (25)

1a	1d9kD01	D:2-92
1b	1d9kH01	H:2-92
1c	1d9kC01	C:3-81
1d	1d9kG01	G:3-81

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

House mouse (Mus musculus) (616)

2a	1d9kB00	B:3-116C
2b	1d9kF00	F:3-116C
2c	1d9kC02	C:82-181
2d	1d9kG02	G:82-181
2e	1d9kD02	D:93-190
2f	1d9kH02	H:93-190
2g	1d9kA00	A:2-117
2h	1d9kE00	E:2-117

(no "Pfam Domain" information available for 1D9K)

Asymmetric Unit(hide GO term definitions)

Chain B,F (TVB5_MOUSE | P04213)

Chain C,G (HA2K_MOUSE | P01910)

molecular function
	GO:0042605	peptide antigen binding	Interacting selectively and non-covalently with an antigen peptide.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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:0048002	antigen processing and presentation of peptide antigen	The process in which an antigen-presenting cell expresses peptide antigen in association with an MHC protein complex on its cell surface, including proteolysis and transport steps for the peptide antigen both prior to and following assembly with the MHC protein complex. The peptide antigen is typically, but not always, processed from an endogenous or exogenous 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:0045582	positive regulation of T cell differentiation	Any process that activates or increases the frequency, rate or extent of T cell differentiation.
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:0009897	external side of plasma membrane	The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
	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: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.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain D,H (HB2K_MOUSE | P06343)

molecular function
	GO:0042605	peptide antigen binding	Interacting selectively and non-covalently with an antigen peptide.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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:0048002	antigen processing and presentation of peptide antigen	The process in which an antigen-presenting cell expresses peptide antigen in association with an MHC protein complex on its cell surface, including proteolysis and transport steps for the peptide antigen both prior to and following assembly with the MHC protein complex. The peptide antigen is typically, but not always, processed from an endogenous or exogenous 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:0002455	humoral immune response mediated by circulating immunoglobulin	An immune response dependent upon secreted immunoglobulin. An example of this process is found in Mus musculus.
	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:0002381	immunoglobulin production involved in immunoglobulin mediated immune response	The appearance of immunoglobulin due to biosynthesis or secretion following a cellular stimulus during an immune response, resulting in an increase in its intracellular or extracellular levels.
cellular component
	GO:0005794	Golgi apparatus	A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
	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:0005769	early endosome	A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
	GO:0009897	external side of plasma membrane	The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
	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:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005771	multivesicular body	A type of endosome in which regions of the limiting endosomal membrane invaginate to form internal vesicles; membrane proteins that enter the internal vesicles are sequestered from the cytoplasm.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain P,Q (TRFE_CHICK | P02789)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0006953	acute-phase response	An acute inflammatory response that involves non-antibody proteins whose concentrations in the plasma increase in response to infection or injury of homeothermic animals.
	GO:0006811	ion transport	The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0055072	iron ion homeostasis	Any process involved in the maintenance of an internal steady state of iron ions within an organism or cell.
	GO:0032496	response to lipopolysaccharide	Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0031012	extracellular matrix	A structure lying external to one or more cells, which provides structural support for cells or tissues.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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	1d9k
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	HA2K_MOUSE \| P01910	:	1iak 1jl4
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	TRFE_CHICK \| P02789	:	1aiv 1iej 1iq7 1jl4 1n04 1nft 1nnt 1ovt 1ryx 1tfa 2d3i
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(no "Related Entries Specified in the PDB File" available for 1D9K)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 10)

Sites (10, 10)

SS Bonds (10, 10)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 2)

PROSITE Motifs (1, 4)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (6, 12)

CATH Domains (2, 12)

Pfam Domains (0, 0)

Gene Ontology (30, 43)

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Related Entries Specified in the PDB File