4M93 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   UNLIGANDED 2 CRYSTAL STRUCTURE OF S25-26 FAB

Authors :   O. Haji-Ghassemi, S. V. Evans

Date :   14 Aug 13 (Deposition) - 09 Apr 14 (Release) - 09 Jul 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.09

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

Keywords :   Carbohydrate/Sugar Binding, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   O. Haji-Ghassemi, S. Muller-Loennies, R. Saldova, M. Muniyappa, L. Brade, P. M. Rudd, D. J. Harvey, P. Kosma, H. Brade, S. V. Evans
Groove-Type Recognition Of Chlamydiaceae-Specific Lipopolysaccharide Antigen By A Family Of Antibodies Possessing An Unusual Variable Heavy Chain N-Linked Glycan.
J. Biol. Chem. V. 289 16644 2014
PubMed-ID: 24682362 | Reference-DOI: 10.1074/JBC.M113.528224

Molecule 1 - S25-26 FAB (IGG1K) LIGHT CHAIN
	Chains	:	L, C
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Strain	:	BALB/C

Molecule 2 - S25-26 FAB (IGG1K) HEAVY CHAIN
	Chains	:	H, B
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Strain	:	BALB/C

		1	2	3	4
Asymmetric Unit	:	B	C	H	L
Biological Unit 1 (1x)	:			H	L
Biological Unit 2 (1x)	:	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 8)

No.	Name	Count	Type	Full Name
1	ACT	3	Ligand/Ion	ACETATE ION
2	CA	1	Ligand/Ion	CALCIUM ION
3	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	PCA	2	Mod. Amino Acid	PYROGLUTAMIC ACID

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	ACT	-1	Ligand/Ion	ACETATE ION
2	CA	-1	Ligand/Ion	CALCIUM ION
3	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID

Biological Unit 2 (3, 5)

No.	Name	Count	Type	Full Name
1	ACT	3	Ligand/Ion	ACETATE ION
2	CA	-1	Ligand/Ion	CALCIUM ION
3	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR B:57 , ASP B:58 , HOH B:462 , HOH B:470 , HOH B:471 , THR C:202	BINDING SITE FOR RESIDUE CA B 302
2	AC2	SOFTWARE	GLY B:127 , SER B:128 , ALA B:129 , ALA B:130 , ACT B:304 , PHE C:209 , ASN C:210 , GLU C:213	BINDING SITE FOR RESIDUE ACT B 303
3	AC3	SOFTWARE	GLY B:127 , SER B:128 , ARG B:213 , ACT B:303 , HOH B:463 , PRO C:119 , ASN C:210 , GLU C:213	BINDING SITE FOR RESIDUE ACT B 304
4	AC4	SOFTWARE	SER B:19 , ILE B:20 , THR B:21 , PHE B:79 , PHE B:80 , LYS B:81	BINDING SITE FOR RESIDUE ACT B 305
5	AC5	SOFTWARE	LYS B:43 , GLN B:83 , ASN B:85	BINDING SITE FOR MONO-SACCHARIDE NAG B 301 BOUND TO ASN B 85
6	AC6	SOFTWARE	LYS H:43 , ASN H:85 , HOH H:456	BINDING SITE FOR MONO-SACCHARIDE NAG H 301 BOUND TO ASN H 85

Asymmetric Unit

No.	Residues
1	B:22	-	B:92
2	B:140	-	B:195
3	C:23	-	C:88
4	C:134	-	C: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	Thr L:7	-	Pro L:8
2	Val L:94	-	Pro L:95
3	Tyr L:140	-	Pro L:141
4	Phe H:146	-	Pro H:147
5	Glu H:148	-	Pro H:149
6	Trp H:188	-	Pro H:189
7	Thr C:7	-	Pro C:8
8	Val C:94	-	Pro C:95
9	Tyr C:140	-	Pro C:141
10	Phe B:146	-	Pro B:147
11	Glu B:148	-	Pro B:149
12	Trp B:188	-	Pro B:189

(no "SAP(SNP)/Variant" information available for 4M93)

(no "PROSITE Motif" information available for 4M93)

(no "Exon" information available for 4M93)

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 B from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                           
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee...ee.....eeeeee..........eeeeeee...eeeeeeee.....eee.......eeeeeehhh.eeeeee...hhhhheeeeee...............eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4m93 B    1 xVQLKESGPGLVQPSQSLSITCTVSGFSLTTYGVHWVRQSPGKGLEWLGVIWSGGSTDYNAAFISRLSISKDNSKSHVFFKMNSLQANDTAIYYCARMRITTDWFAYWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR  213
                            |       10        20        30        40        50        60        70        80  |||   87        97   ||  105       115       125       135       145       155       165       175       185       195       205        
                            |                                                                               82A||               100A|                                                                                                                 
                            1-PCA                                                                            82B|                100B                                                                                                                 
                                                                                                              82C

Chain C from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                           
               SCOP domains d4m93c1 C:1-107 automated matches                                                                               d4m93c2 C:108-213 automated matches                                                                        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.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4m93 C    1 DILMNQTPLSLPVSLGDQASISCRSSQYIVHRNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPYTFGGGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE  213
                                    10        20       27C||      35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205        
                                                     27A||||                                                                                                                                                                                          
                                                      27B|||                                                                                                                                                                                          
                                                       27C||                                                                                                                                                                                          
                                                        27D|                                                                                                                                                                                          
                                                         27E

Chain H from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                           
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........eeeeeee...eeeeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeee...............eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4m93 H    1 xVQLKESGPGLVQPSQSLSITCTVSGFSLTTYGVHWVRQSPGKGLEWLGVIWSGGSTDYNAAFISRLSISKDNSKSHVFFKMNSLQANDTAIYYCARMRITTDWFAYWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR  213
                            |       10        20        30        40        50        60        70        80  |||   87        97   ||  105       115       125       135       145       155       165       175       185       195       205        
                            1-PCA                                                                           82A||               100A|                                                                                                                 
                                                                                                             82B|                100B                                                                                                                 
                                                                                                              82C

Chain L from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                           
               SCOP domains d4m93l1 L:1-107 automated matches                                                                               d4m93l2 L:108-213 automated matches                                                                        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..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeeee..eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4m93 L    1 DILMNQTPLSLPVSLGDQASISCRSSQYIVHRNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPYTFGGGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE  213
                                    10        20       27C||      35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205        
                                                     27A||||                                                                                                                                                                                          
                                                      27B|||                                                                                                                                                                                          
                                                       27C||                                                                                                                                                                                          
                                                        27D|                                                                                                                                                                                          
                                                         27E

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)

Mouse (Mus musculus) [TaxId: 10090] (309)

1a	d4m93c2	C:108-213
1b	d4m93l2	L:108-213

Family: V set domains (antibody variable domain-like) (1919)

Protein domain: automated matches (311)

Mouse (Mus musculus) [TaxId: 10090] (112)

2a	d4m93c1	C:1-107
2b	d4m93l1	L:1-107

(no "CATH Domain" information available for 4M93)

(no "Pfam Domain" information available for 4M93)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 4M93)

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

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	4m93
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4m7j	SAME PROTEIN, UNLIGANDED
4m7z	SAME PROTEIN, UNLIGANDED STRUCTURE 2
4ma1	SAME PROTEIN, UNLIGANDED STRUCTURE 3

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 8)

Sites (6, 6)

SS Bonds (8, 8)

Cis Peptide Bonds (12, 12)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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SCOP Domains (2, 4)

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