4MA1 - 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)

Title :   UNLIGANDED 3 CRYSTAL STRUCTURE OF S25-26 FAB

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

Date :   15 Aug 13 (Deposition) - 09 Apr 14 (Release) - 09 Jul 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.32

Chains :   Asym. Unit : B,C,E,F,H,L
Biol. Unit 1: B,C  (1x)
Biol. Unit 2: E,F  (1x)
Biol. Unit 3: H,L  (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) HEAVY CHAIN
	Chains	:	B, E, H
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Strain	:	BALB/C

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

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (9, 24)

No.	Name	Count	Type	Full Name
1	BMA	3	Ligand/Ion	BETA-D-MANNOSE
2	FUC	3	Ligand/Ion	ALPHA-L-FUCOSE
3	GAL	1	Ligand/Ion	BETA-D-GALACTOSE
4	GLA	1	Ligand/Ion	ALPHA D-GALACTOSE
5	K	1	Ligand/Ion	POTASSIUM ION
6	MAN	4	Ligand/Ion	ALPHA-D-MANNOSE
7	NAG	7	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
8	PCA	2	Mod. Amino Acid	PYROGLUTAMIC ACID
9	PEG	2	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 1 (6, 7)

No.	Name	Count	Type	Full Name
1	BMA	1	Ligand/Ion	BETA-D-MANNOSE
2	FUC	1	Ligand/Ion	ALPHA-L-FUCOSE
3	GAL	-1	Ligand/Ion	BETA-D-GALACTOSE
4	GLA	-1	Ligand/Ion	ALPHA D-GALACTOSE
5	K	-1	Ligand/Ion	POTASSIUM ION
6	MAN	1	Ligand/Ion	ALPHA-D-MANNOSE
7	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
8	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID
9	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 2 (4, 5)

No.	Name	Count	Type	Full Name
1	BMA	1	Ligand/Ion	BETA-D-MANNOSE
2	FUC	1	Ligand/Ion	ALPHA-L-FUCOSE
3	GAL	-1	Ligand/Ion	BETA-D-GALACTOSE
4	GLA	-1	Ligand/Ion	ALPHA D-GALACTOSE
5	K	-1	Ligand/Ion	POTASSIUM ION
6	MAN	1	Ligand/Ion	ALPHA-D-MANNOSE
7	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
8	PCA	-1	Mod. Amino Acid	PYROGLUTAMIC ACID
9	PEG	-1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 3 (8, 11)

No.	Name	Count	Type	Full Name
1	BMA	1	Ligand/Ion	BETA-D-MANNOSE
2	FUC	1	Ligand/Ion	ALPHA-L-FUCOSE
3	GAL	1	Ligand/Ion	BETA-D-GALACTOSE
4	GLA	1	Ligand/Ion	ALPHA D-GALACTOSE
5	K	-1	Ligand/Ion	POTASSIUM ION
6	MAN	2	Ligand/Ion	ALPHA-D-MANNOSE
7	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
8	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID
9	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP B:58 , HOH B:534	BINDING SITE FOR RESIDUE PEG B 406
2	AC2	SOFTWARE	TRP H:52 , SER H:56 , HOH H:559	BINDING SITE FOR RESIDUE PEG H 410
3	AC3	SOFTWARE	TYR L:27A , HIS L:27D , SER L:67 , HOH L:443 , HOH L:444	BINDING SITE FOR RESIDUE K L 301
4	AC4	SOFTWARE	LYS B:43 , ASN B:85	BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 85 RESIDUES 401 TO 405
5	AC5	SOFTWARE	THR B:192 , THR B:194 , LYS B:209 , LYS E:43 , ASN E:85	BINDING SITE FOR CHAIN E OF SUGAR BOUND TO ASN E 85 RESIDUES 401 TO 405
6	AC6	SOFTWARE	THR B:30 , SER F:56 , GLY F:57 , ARG H:38 , ASN H:85 , ASP H:207 , LYS H:209 , GLU L:123	BINDING SITE FOR CHAIN H OF SUGAR BOUND TO ASN H 85 RESIDUES 401 TO 409

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	E:22	-	E:92
6	E:140	-	E:195
7	F:23	-	F:88
8	F:134	-	F:194
9	H:22	-	H:92
10	H:140	-	H:195
11	L:23	-	L:88
12	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	Gly E:54	-	Gly E:55
5	Ile E:64	-	Ser E:65
6	Phe E:146	-	Pro E:147
7	Glu E:148	-	Pro E:149
8	Trp E:188	-	Pro E:189
9	Phe H:146	-	Pro H:147
10	Glu H:148	-	Pro H:149
11	Trp H:188	-	Pro H:189
12	Thr C:7	-	Pro C:8
13	Val C:94	-	Pro C:95
14	Tyr C:140	-	Pro C:141
15	Thr F:7	-	Pro F:8
16	Val F:94	-	Pro F:95
17	Tyr F:140	-	Pro F:141
18	Thr L:7	-	Pro L:8
19	Val L:94	-	Pro L:95
20	Tyr L:140	-	Pro L:141

(no "SAP(SNP)/Variant" information available for 4MA1)

(no "PROSITE Motif" information available for 4MA1)

(no "Exon" information available for 4MA1)

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 ..eeeee...ee.....eeeeeeee........eeeeeee...eeeeeeee.....eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeee...............eeeee........eeeee..........eeeeeeeeeee.....eeee........eee...eee..eeeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ma1 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:219
                                                                                                                                                                                                                                                            
               SCOP domains d4ma1c1 C:1-107 automated matches                                                                               d4ma1c2 C:108-214 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..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.hhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ma1 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 E from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee...ee.....eeeeee..........eeeeeee...eeeeeeee.....eee.......eeee......eeeeee...hhhhheeeeee...............eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.hhh.....eeeeee....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4ma1 E    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 F from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                            
               SCOP domains d4ma1f1 F:1-107 automated matches                                                                               d4ma1f2 F: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..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeeee..eeeeeeeeee.hhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ma1 F    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:218
                                                                                                                                                                                                                                                           
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee...ee.....eeeeee..........eeeeeee...eeeeeeee.....eee.hhhh..eeeeee....eeeeee...hhhhheeeeee...............eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ma1 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:219
                                                                                                                                                                                                                                                            
               SCOP domains d4ma1l1 L:1-107 automated matches                                                                               d4ma1l2 L: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..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.hhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ma1 L    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

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	d4ma1c2	C:108-214
1b	d4ma1f2	F:108-214
1c	d4ma1l2	L:108-214

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

Protein domain: automated matches (311)

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

2a	d4ma1c1	C:1-107
2b	d4ma1f1	F:1-107
2c	d4ma1l1	L:1-107

(no "CATH Domain" information available for 4MA1)

(no "Pfam Domain" information available for 4MA1)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 4MA1)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Glu B:148 - Pro B:149	[ RasMol ]
		Glu E:148 - Pro E:149	[ RasMol ]
		Glu H:148 - Pro H:149	[ RasMol ]
		Gly E:54 - Gly E:55	[ RasMol ]
		Ile E:64 - Ser E:65	[ RasMol ]
		Phe B:146 - Pro B:147	[ RasMol ]
		Phe E:146 - Pro E:147	[ RasMol ]
		Phe H:146 - Pro H:147	[ RasMol ]
		Thr C:7 - Pro C:8	[ RasMol ]
		Thr F:7 - Pro F:8	[ RasMol ]
		Thr L:7 - Pro L:8	[ RasMol ]
		Trp B:188 - Pro B:189	[ RasMol ]
		Trp E:188 - Pro E:189	[ RasMol ]
		Trp H:188 - Pro H:189	[ RasMol ]
		Tyr C:140 - Pro C:141	[ RasMol ]
		Tyr F:140 - Pro F:141	[ RasMol ]
		Tyr L:140 - Pro L:141	[ RasMol ]
		Val C:94 - Pro C:95	[ RasMol ]
		Val F:94 - Pro F:95	[ RasMol ]
		Val L:94 - Pro L:95	[ RasMol ]

Biological Units
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		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

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	4ma1
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4m7j	SAME PROTEIN IN COMPLEX WITH KDO(2.8)KDO(2.4)KDO TRISACCHARIDE
4m7z	SAME PROTEIN, UNLIGANDED STRUCTURE 1
4m93	SAME PROTEIN, UNLIGANDED STRUCTURE 2

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (9, 24)

Sites (6, 6)

SS Bonds (12, 12)

Cis Peptide Bonds (20, 20)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (2, 6)

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