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Title :   CRYSTAL STRUCTURE OF A FAB FRAGMENT WITH ITS LIGAND PEPTIDE

Authors :   Y. Kitago, K. K. Kaneko, S. Ogasawara, Y. Kato, J. Takagi

Date :   24 Jun 16 (Deposition) - 14 Sep 16 (Release) - 14 Sep 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.93

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

Keywords :   Fab, Peptide Ligand, Mutation, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Kitago, M. K. Kaneko, S. Ogasawara, Y. Kato, J. Takagi
Structural Basis For Multi-Specific Peptide Recognition By The Anti-Idh1/2 Monoclonal Antibody, Msmab-1.
Biochem. Biophys. Res. Commun. 2016
PubMed-ID: 27553275 | Reference-DOI: 10.1016/J.BBRC.2016.08.110

Molecule 1 - HEAVY CHAIN OF FAB FRAGMENT
	Chains	:	H, A
	Engineered	:	YES
	Expression System	:	MAMMALIA
	Expression System Cell	:	HYBRIDOMA
	Expression System Taxid	:	40674
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 2 - LIGHT CHAIN OF FAB FRAGMENT
	Chains	:	L, B
	Engineered	:	YES
	Expression System	:	MAMMALIA
	Expression System Cell	:	HYBRIDOMA
	Expression System Taxid	:	40674
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 3 - LYS-PRO-ILE-ILE-ILE-GLY-SER-HIS-ALA-TYR-GLY-ASP
	Chains	:	C, D
	Engineered	:	YES
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 13)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
2	PCA	2	Mod. Amino Acid	PYROGLUTAMIC ACID
3	SO4	9	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 7)

No.	Name	Count	Type	Full Name
1	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
2	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID
3	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 6)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
2	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID
3	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	SO4 A:301 , ARG H:58 , SER L:93 , TRP L:94	binding site for residue SO4 H 301
02	AC2	SOFTWARE	SER H:161 , GLY H:162 , HOH H:420	binding site for residue SO4 H 302
03	AC3	SOFTWARE	ARG H:213 , HOH H:407 , HOH H:447 , SER L:122	binding site for residue SO4 H 303
04	AC4	SOFTWARE	THR L:182 , ARG L:188	binding site for residue SO4 L 301
05	AC5	SOFTWARE	ASP L:17 , SER L:18 , HOH L:408	binding site for residue SO4 L 302
06	AC6	SOFTWARE	PRO L:8 , ALA L:9 , THR L:10	binding site for residue SO4 L 303
07	AC7	SOFTWARE	ARG A:58 , SER B:93 , TRP B:94 , SO4 H:301	binding site for residue SO4 A 301
08	AC8	SOFTWARE	SER A:120 , EDO A:303 , HOH A:407 , SER H:120 , HOH H:469	binding site for residue SO4 A 302
09	AC9	SOFTWARE	SER A:120 , VAL A:121 , SO4 A:302 , HOH A:441 , ALA H:118 , THR H:204	binding site for residue EDO A 303
10	AD1	SOFTWARE	ALA A:118 , HOH A:407 , HOH A:455 , SER H:120 , VAL H:121 , LYS H:208	binding site for residue EDO A 304
11	AD2	SOFTWARE	GLN B:27 , ARG B:28 , HOH B:456	binding site for residue SO4 B 301

Asymmetric Unit

No.	Residues
1	A:22	-	A:92
2	A:140	-	A:195
3	B:23	-	B:88
4	B:134	-	B:194
5	H:22	-	H:92
6	H:140	-	H:195
7	L:23	-	L:88
8	L:134	-	L:194

Asymmetric Unit

No.	Residues
1	Phe H:146	-	Pro H:147
2	Glu H:148	-	Pro H:149
3	Trp H:188	-	Pro H:189
4	Ser L:7	-	Pro L:8
5	Trp L:94	-	Pro L:95
6	Tyr L:140	-	Pro L:141
7	Phe A:146	-	Pro A:147
8	Glu A:148	-	Pro A:149
9	Trp A:188	-	Pro A:189
10	Ser B:7	-	Pro B:8
11	Trp B:94	-	Pro B:95
12	Tyr B:140	-	Pro B:141

(no "SAP(SNP)/Variant" information available for 5GIR)

(no "PROSITE Motif" information available for 5GIR)

(no "Exon" information available for 5GIR)

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:207
                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eeee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.......eeeeeehhh.eeeeee...hhhhheeeeee.........eeeee........eeeee.....eeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeehhhhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gir A   1 xVQLQQPGAELVRPGASVKLSCKASGYTFTSYWMNWVKQRPGQGLECIGMIHPSDGETRLNQKFKDKATLTLDKSSSTAYMQLSSPTSEDSAVYYCTTHFDYWGQGTTLTVSSAKTTAPSVYPLAPVCSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR 213
                            |       10        20        30        40        50  |     59        69        79   |||  86        96|      110       120       136       146       156       166       176       186       196       206       
                            |                                                 52A                            82A||            96|                        128|                                                                              
                            1-PCA                                                                             82B|            101                         135                                                                              
                                                                                                               82C

Chain B from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee....eeeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeeee......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gir B   1 DIVLIQSPATLSVTPGDSVSLSCRASQRISNNLHWYQQKSHESPRLLIRYTSQSISGIPSRFSGSGSGTDFTLSINSVETEDFGMYFCQQSNSWPFTFGSGTKLEMKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR 211
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain C from PDB  Type:PROTEIN  Length:12
                                            
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author .....hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 5gir C 126 KPIIIGSHAYGD 137
                                   135

Chain D 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
                 5gir D 126 KPIIIGSHAY 135
                                   135

Chain H from PDB  Type:PROTEIN  Length:209
                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eeee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeee.........eeeee........eeeee......eeeeeeeeeee.....eeee.hhh....eee...ee....eeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gir H   1 xVQLQQPGAELVRPGASVKLSCKASGYTFTSYWMNWVKQRPGQGLECIGMIHPSDGETRLNQKFKDKATLTLDKSSSTAYMQLSSPTSEDSAVYYCTTHFDYWGQGTTLTVSSAKTTAPSVYPLAPVCGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR 213
                            |       10        20        30        40        50  |     59        69        79   |||  86        96|      110       120       134       144       154       164       174       184       194       204         
                            1-PCA                                             52A                            82A||            96|                        128|                                                                                
                                                                                                              82B|            101                         133                                                                                
                                                                                                               82C

Chain L from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee....eeeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeeee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gir L   1 DIVLIQSPATLSVTPGDSVSLSCRASQRISNNLHWYQQKSHESPRLLIRYTSQSISGIPSRFSGSGSGTDFTLSINSVETEDFGMYFCQQSNSWPFTFGSGTKLEMKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN 212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

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 5GIR)

(no "CATH Domain" information available for 5GIR)

(no "Pfam Domain" information available for 5GIR)

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Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Glu A:148 - Pro A:149	[ RasMol ]
		Glu H:148 - Pro H:149	[ RasMol ]
		Phe A:146 - Pro A:147	[ RasMol ]
		Phe H:146 - Pro H:147	[ RasMol ]
		Ser B:7 - Pro B:8	[ RasMol ]
		Ser L:7 - Pro L:8	[ RasMol ]
		Trp A:188 - Pro A:189	[ RasMol ]
		Trp B:94 - Pro B:95	[ RasMol ]
		Trp H:188 - Pro H:189	[ RasMol ]
		Trp L:94 - Pro L:95	[ RasMol ]
		Tyr B:140 - Pro B:141	[ RasMol ]
		Tyr L:140 - Pro L:141	[ RasMol ]

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		Biological Unit 2	[ Jena3D ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 13)

Sites (11, 11)

SS Bonds (8, 8)

Cis Peptide Bonds (12, 12)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (30, 30)

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