4GKN - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   A2-MHC COMPLEX CARRYING FATGIGIITV

Authors :   A. K. Sewell, P. J. Rizkallah, D. K. Cole, L. Wooldridge, D. A. Price

Date :   13 Aug 12 (Deposition) - 12 Sep 12 (Release) - 14 Nov 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.75

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

Keywords :   Major Histocompatibility Complex, T-Cell Receptor, Immuno, Immunoglobulin, Recognition, Mhc, Tcr, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Ekeruche-Makinde, M. Clement, D. K. Cole, E. S. Edwards, K. Ladell, J. J. Miles, K. K. Matthews, A. Fuller, K. A. Lloyd, F. Madura, G. M. Dolton, J. Pentier, A. Lissina, E. Gostick, T. K. Baxter, B. M. Baker, P. J. Rizkallah, D. A. Price, L. Wooldridge, A. K. Sewell
T-Cell Receptor-Optimized Peptide Skewing Of The T-Cell Repertoire Can Enhance Antigen Targeting.
J. Biol. Chem. V. 287 37269 2012
PubMed-ID: 22952231 | Reference-DOI: 10.1074/JBC.M112.386409

Molecule 1 - HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
	Chains	:	A, D
	Engineered	:	YES
	Gene	:	HLA-A, HLAA
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	MHC CLASS I ANTIGEN A*2

Molecule 2 - BETA-2-MICROGLOBULIN
	Chains	:	B, E
	Engineered	:	YES
	Gene	:	B2M
	Organism Common	:	LOWLAND GORILLA
	Organism Scientific	:	GORILLA GORILLA GORILLA
	Organism Taxid	:	9595

Molecule 3 - FAT COGNATE PEPTIDE
	Chains	:	C, F
	Engineered	:	YES
	Organism Scientific	:	SYNTHETIC CONSTRUCT
	Organism Taxid	:	32630
	Synthetic	:	YES

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A	B	C
Biological Unit 2 (1x)	:				D	E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 8)

No.	Name	Count	Type	Full Name
1	SO4	8	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:142 , HIS A:145	BINDING SITE FOR RESIDUE SO4 A 301
2	AC2	SOFTWARE	HIS A:191 , HIS A:192 , ALA A:193 , ASN E:17 , GLU E:74	BINDING SITE FOR RESIDUE SO4 A 302
3	AC3	SOFTWARE	TRP A:133 , THR A:134 , ALA A:135 , GLN A:141 , LYS A:144	BINDING SITE FOR RESIDUE SO4 A 303
4	AC4	SOFTWARE	GLU A:232 , THR A:233	BINDING SITE FOR RESIDUE SO4 A 304
5	AC5	SOFTWARE	THR D:142 , HIS D:145	BINDING SITE FOR RESIDUE SO4 D 301
6	AC6	SOFTWARE	ASN B:17 , GLU B:74 , HIS D:191 , HIS D:192 , ALA D:193	BINDING SITE FOR RESIDUE SO4 D 302
7	AC7	SOFTWARE	ARG E:12 , HIS E:13 , PHE E:22	BINDING SITE FOR RESIDUE SO4 E 101
8	AC8	SOFTWARE	LYS E:41 , THR E:71 , TYR E:78	BINDING SITE FOR RESIDUE SO4 E 102

Asymmetric Unit

No.	Residues
1	A:101	-	A:164
2	A:203	-	A:259
3	B:25	-	B:80
4	D:101	-	D:164
5	D:203	-	D:259
6	E:25	-	E:80

Asymmetric Unit

No.	Residues
1	Tyr A:209	-	Pro A:210
2	His B:31	-	Pro B:32
3	Tyr D:209	-	Pro D:210
4	His E:31	-	Pro E:32

(no "SAP(SNP)/Variant" information available for 4GKN)

(no "PROSITE Motif" information available for 4GKN)

(no "Exon" information available for 4GKN)

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:276
                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeee........eeeeeeee..eeeeeee........ee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeeeeee.....eeeeeeeeee..eeeeee......eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeeee..eeeeeeeeeee.......eee.........eee...ee.....eeeeeeeeee.......eeee........eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4gkn A   1 GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDGKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEP 276
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270

Chain B from PDB  Type:PROTEIN  Length:100
                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee.........eeeeeeeeee.....eeeeee..ee....ee...ee.....eeeeeeeee.......eeeeee.......eeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 4gkn B   0 MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM  99
                                     9        19        29        39        49        59        69        79        89        99

Chain C from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 4gkn C   1 FATGIGIITV  10
                                    10

Chain D from PDB  Type:PROTEIN  Length:276
                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeeee........eeeeeeee..eeeeeee........ee.hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeeeeeee.....eeeeeeeeee..eeeeee......eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeee....eeeeeeeeeee.....eeeeee........eee...ee.....eeeeeeeeee..hhh.eeeeee.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4gkn D   1 GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDGKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEP 276
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270

Chain E from PDB  Type:PROTEIN  Length:100
                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee.........eeeeeeeeee.....eeeeee..ee....ee...ee.....eeeeeeeee.......eeeeee.......eeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 4gkn E   0 MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM  99
                                     9        19        29        39        49        59        69        79        89        99

Chain F from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 4gkn F   1 FATGIGIITV  10
                                    10

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 '\|'

(no "SCOP Domain" information available for 4GKN)

(no "CATH Domain" information available for 4GKN)

(no "Pfam Domain" information available for 4GKN)

Asymmetric Unit(hide GO term definitions)

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		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		His B:31 - Pro B:32	[ RasMol ]
		His E:31 - Pro E:32	[ RasMol ]
		Tyr A:209 - Pro A:210	[ RasMol ]
		Tyr D:209 - Pro D:210	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 8)

Sites (8, 8)

SS Bonds (6, 6)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (0, 0)

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Gene Ontology (72, 99)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File