4M7Z - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   UNLIGANDED 1 CRYSTAL STRUCTURE OF S25-26 FAB

Authors :   O. Haji-Ghassemi, S. V. Evans, S. Muller-Loennies, R. Saldova, M. Muni L. Brade, P. M. Rudd, D. J. Harvey, P. Kosma, H. Brade

Date :   12 Aug 13 (Deposition) - 09 Apr 14 (Release) - 09 Jul 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.75

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

Keywords :   Beta-Sandwich, 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) HEAVY CHAIN
	Chains	:	B, H
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Strain	:	BALB/C

Molecule 2 - S25-26 FAB (IGG1K) LIGHT CHAIN
	Chains	:	C, L
	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)	:	B	C
Biological Unit 2 (1x)	:			H	L

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 19)

No.	Name	Count	Type	Full Name
1	CA	3	Ligand/Ion	CALCIUM ION
2	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	PEG	6	Ligand/Ion	DI(HYDROXYETHYL)ETHER
4	PG4	8	Ligand/Ion	TETRAETHYLENE GLYCOL

Biological Unit 1 (3, 10)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	PEG	4	Ligand/Ion	DI(HYDROXYETHYL)ETHER
4	PG4	5	Ligand/Ion	TETRAETHYLENE GLYCOL

Biological Unit 2 (3, 6)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	PEG	2	Ligand/Ion	DI(HYDROXYETHYL)ETHER
4	PG4	3	Ligand/Ion	TETRAETHYLENE GLYCOL

Asymmetric Unit (18, 18)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN B:85	BINDING SITE FOR RESIDUE NAG B 401
02	AC2	SOFTWARE	SER B:7 , LYS B:75 , HIS B:77 , ASN H:82A	BINDING SITE FOR RESIDUE PG4 B 402
03	AC3	SOFTWARE	SER B:65 , ASN B:82A , HOH B:538 , LYS H:75 , HIS H:77	BINDING SITE FOR RESIDUE PG4 B 403
04	AC4	SOFTWARE	TRP B:52 , THR B:57 , ASP B:58 , CA B:409	BINDING SITE FOR RESIDUE PG4 B 404
05	AC5	SOFTWARE	GLN B:39 , PRO B:41 , ILE B:89 , LEU B:108 , GLU B:148 , ALA B:168	BINDING SITE FOR RESIDUE PG4 B 405
06	AC6	SOFTWARE	GLU B:6 , SER B:7 , GLY B:8 , GLY B:10 , GLY B:106 , THR B:107 , LEU B:108	BINDING SITE FOR RESIDUE PEG B 406
07	AC7	SOFTWARE	LYS B:43 , HOH C:434	BINDING SITE FOR RESIDUE PEG B 408
08	AC8	SOFTWARE	ASP B:58 , PG4 B:404	BINDING SITE FOR RESIDUE CA B 409
09	AC9	SOFTWARE	ASN H:85	BINDING SITE FOR RESIDUE NAG H 401
10	BC1	SOFTWARE	THR H:57 , ASP H:58 , CA H:404	BINDING SITE FOR RESIDUE PG4 H 402
11	BC2	SOFTWARE	GLN H:105 , GLY H:106	BINDING SITE FOR RESIDUE PEG H 403
12	BC3	SOFTWARE	ASP H:58 , PG4 H:402	BINDING SITE FOR RESIDUE CA H 404
13	BC4	SOFTWARE	GLN C:18 , SER C:20 , LYS C:74	BINDING SITE FOR RESIDUE PG4 C 301
14	BC5	SOFTWARE	LEU C:9 , TYR C:87 , GLY C:100 , GLY C:101 , HOH C:430 , HOH C:437	BINDING SITE FOR RESIDUE PEG C 302
15	BC6	SOFTWARE	GLY H:42 , LEU L:9 , TYR L:87 , GLY L:100 , LYS L:103	BINDING SITE FOR RESIDUE PG4 L 301
16	BC7	SOFTWARE	LYS L:74	BINDING SITE FOR RESIDUE PG4 L 302
17	BC8	SOFTWARE	PHE L:98	BINDING SITE FOR RESIDUE PEG L 303
18	BC9	SOFTWARE	GLU C:79 , GLU C:81 , GLU L:79 , GLU L:81	BINDING SITE FOR RESIDUE CA L 304

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	Phe B:146	-	Pro B:147
2	Glu B:148	-	Pro B:149
3	Trp B:188	-	Pro B:189
4	Pro H:14	-	Ser H:15
5	Phe H:146	-	Pro H:147
6	Glu H:148	-	Pro H:149
7	Trp H:188	-	Pro H:189
8	Thr C:7	-	Pro C:8
9	Val C:94	-	Pro C:95
10	Tyr C:140	-	Pro C:141
11	Thr L:7	-	Pro L:8
12	Val L:94	-	Pro L:95
13	Tyr L:140	-	Pro L:141

(no "SAP(SNP)/Variant" information available for 4M7Z)

(no "PROSITE Motif" information available for 4M7Z)

(no "Exon" information available for 4M7Z)

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:216
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee...ee.....eeeeee..........eeeeee.....eeeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeee...............eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4m7z B    4 LKESGPGLVQPSQSLSITCTVSGFSLTTYGVHWVRQSPGKGLEWLGVIWSGGSTDYNAAFISRLSISKDNSKSHVFFKMNSLQANDTAIYYCARMRITTDWFAYWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRD  214
                                    13        23        33        43        53        63        73       82A||      90       100||     108       118       128       138       148       158       168       178       188       198       208      
                                                                                                         82A||               100A|                                                                                                                  
                                                                                                          82B|                100B                                                                                                                  
                                                                                                           82C

Chain C from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                            
               SCOP domains d4m7zc1 C:1-107 automated matches                                                                               d4m7zc2 C:108-214 automated matches                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee............eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee....eeeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeeee......eeeeee.hhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4m7z C    1 DILMNQTPLSLPVSLGDQASISCRSSQYIVHRNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPYTFGGGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  214
                                    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:215
                                                                                                                                                                                                                                                        
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...ee.....eeeeee..........eeeeee.....eeeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeee...............eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4m7z H    4 LKESGPGLVQPSQSLSITCTVSGFSLTTYGVHWVRQSPGKGLEWLGVIWSGGSTDYNAAFISRLSISKDNSKSHVFFKMNSLQANDTAIYYCARMRITTDWFAYWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR  213
                                    13        23        33        43        53        63        73       82A||      90       100||     108       118       128       138       148       158       168       178       188       198       208     
                                                                                                         82A||               100A|                                                                                                                 
                                                                                                          82B|                100B                                                                                                                 
                                                                                                           82C

Chain L from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                           
               SCOP domains d4m7zl1 L:1-107 automated matches                                                                               d4m7zl2 L:108-213 automated matches                                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee............eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee....eeeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeeee......eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4m7z 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)
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	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	d4m7zc2	C:108-214
1b	d4m7zl2	L:108-213

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

Protein domain: automated matches (311)

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

2a	d4m7zc1	C:1-107
2b	d4m7zl1	L:1-107

(no "CATH Domain" information available for 4M7Z)

(no "Pfam Domain" information available for 4M7Z)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 4M7Z)

Asymmetric Unit
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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 ]
		Pro H:14 - Ser H:15	[ 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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	4m7z
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4m7j	SAME PROTEIN IN COMPLEX WITH KDO(2.8)KDO(2.4)KDO TRISACCHARIDE
4m93	SAME PROTEIN, UNLIGANDED STRUCTURE 2
4ma1	SAME PROTEIN, UNLIGANDED STRUCTURE 3

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 19)

Sites (18, 18)

SS Bonds (8, 8)

Cis Peptide Bonds (13, 13)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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