1JTP - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   DEGENERATE INTERFACES IN ANTIGEN-ANTIBODY COMPLEXES

Authors :   K. Decanniere, T. R. Transue, A. Desmyter, D. Maes, S. Muyldermans, L. Wyns

Date :   21 Aug 01 (Deposition) - 05 Dec 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A,B,L,M
Biol. Unit 1: A,L  (1x)
Biol. Unit 2: B,M  (1x)

Keywords :   Immunoglobulin, Heavy Chain Antibody, Vhh, Interface, Binding, Antibody, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Decanniere, T. R. Transue, A. Desmyter, D. Maes, S. Muyldermans, L. Wyns
Degenerate Interfaces In Antigen-Antibody Complexes.
J. Mol. Biol. V. 313 473 2001
PubMed-ID: 11676532 | Reference-DOI: 10.1006/JMBI.2001.5075
(for further references see the PDB file header)

Molecule 1 - SINGLE-DOMAIN ANTIBODY
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PHEN1
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	VH DOMAIN FRAGMENT
	Organism Common	:	ARABIAN CAMEL
	Organism Scientific	:	CAMELUS DROMEDARIUS
	Organism Taxid	:	9838

Molecule 2 - LYSOZYME C
	Chains	:	L, M
	EC Number	:	3.2.1.17
	Fragment	:	ENZYME
	Organism Common	:	TURKEY
	Organism Scientific	:	MELEAGRIS GALLOPAVO
	Organism Taxid	:	9103
	Other Details	:	PURCHASED FROM SIGMA
	Synonym	:	1,4-BETA-N-ACETYLMURAMIDASE C

		1	2	3	4
Asymmetric Unit	:	A	B	L	M
Biological Unit 1 (1x)	:	A		L
Biological Unit 2 (1x)	:		B		M

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 11)

No.	Name	Count	Type	Full Name
1	FMT	6	Ligand/Ion	FORMIC ACID
2	NA	5	Ligand/Ion	SODIUM ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	FMT	2	Ligand/Ion	FORMIC ACID
2	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	FMT	4	Ligand/Ion	FORMIC ACID
2	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:99 , THR A:101 , GLY A:119 , ASP A:121 , HOH A:510 , HOH A:537	BINDING SITE FOR RESIDUE NA A 501
02	AC2	SOFTWARE	ASP B:99 , THR B:101 , GLY B:119 , ASP B:121 , HOH B:511 , HOH M:559	BINDING SITE FOR RESIDUE NA B 502
03	AC3	SOFTWARE	SER L:60 , CYS L:64 , SER L:72 , LYS L:73 , HOH L:515 , HOH L:568	BINDING SITE FOR RESIDUE NA L 503
04	AC4	SOFTWARE	SER M:60 , CYS M:64 , SER M:72 , LYS M:73 , HOH M:520 , HOH M:533	BINDING SITE FOR RESIDUE NA M 504
05	AC5	SOFTWARE	SER A:105 , GLU L:35 , FMT L:406 , HOH L:526 , HOH L:550 , HOH L:551	BINDING SITE FOR RESIDUE NA L 505
06	AC6	SOFTWARE	ALA A:6 , TYR A:94 , TYR A:95 , CYS A:96 , GLY A:124 , GLY A:126 , THR A:127	BINDING SITE FOR RESIDUE FMT A 401
07	AC7	SOFTWARE	ALA B:6 , TYR B:94 , TYR B:95 , CYS B:96 , GLY B:124 , GLN B:125 , GLY B:126 , THR B:127 , HOH B:566	BINDING SITE FOR RESIDUE FMT B 402
08	AC8	SOFTWARE	ASN M:65 , GLY M:67 , ARG M:68 , THR M:69 , SER M:72 , HOH M:520 , HOH M:533	BINDING SITE FOR RESIDUE FMT M 403
09	AC9	SOFTWARE	HOH B:511 , HOH M:543	BINDING SITE FOR RESIDUE FMT M 404
10	BC1	SOFTWARE	ASN L:113 , ARG L:114 , HOH L:540 , ARG M:5 , CYS M:6 , HOH M:511	BINDING SITE FOR RESIDUE FMT M 405
11	BC2	SOFTWARE	GLU L:35 , VAL L:109 , ALA L:110 , NA L:505 , HOH L:551 , HOH L:571 , HOH L:576	BINDING SITE FOR RESIDUE FMT L 406

Asymmetric Unit

No.	Residues
1	A:22	-	A:96
2	A:33	-	A:109
3	B:22	-	B:96
4	B:33	-	B:109
5	L:6	-	L:127
6	L:30	-	L:115
7	L:64	-	L:80
8	L:76	-	L:94
9	M:6	-	M:127
10	M:30	-	M:115
11	M:64	-	M:80
12	M:76	-	M:94

Asymmetric Unit

No.	Residues
1	Gly A:30	-	Pro A:31
2	Gly B:30	-	Pro B:31

(no "SAP(SNP)/Variant" information available for 1JTP)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LACTALBUMIN_LYSOZYME_2	PS51348	Alpha-lactalbumin / lysozyme C family profile.	LYSC_MELGA	19-147	2	L:1-129 M:1-129
2	LACTALBUMIN_LYSOZYME_1	PS00128	Alpha-lactalbumin / lysozyme C signature.	LYSC_MELGA	94-112	2	L:76-94 M:76-94

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LACTALBUMIN_LYSOZYME_2	PS51348	Alpha-lactalbumin / lysozyme C family profile.	LYSC_MELGA	19-147	1	L:1-129 -
2	LACTALBUMIN_LYSOZYME_1	PS00128	Alpha-lactalbumin / lysozyme C signature.	LYSC_MELGA	94-112	1	L:76-94 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LACTALBUMIN_LYSOZYME_2	PS51348	Alpha-lactalbumin / lysozyme C family profile.	LYSC_MELGA	19-147	1	- M:1-129
2	LACTALBUMIN_LYSOZYME_1	PS00128	Alpha-lactalbumin / lysozyme C signature.	LYSC_MELGA	94-112	1	- M:76-94

(no "Exon" information available for 1JTP)

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:135
                                                                                                                                                                       
               SCOP domains d1jtpa_ A: Camelid IG heavy chain variable domain, VHh                                                                                  SCOP domains
               CATH domains 1jtpA00 A:1-135 Immunoglobulins                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eeee....eeeeeeee.......eeeeeee......eeeeeee.....eee.hhhh..eeeee.....eeeeee...hhhhheeeeeeee.........hhhhhhh......ee...eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jtp A   1 DVQLQASGGGSVQAGGSLRLSCAASGYTIGPYCMGWFRQAPGKEREGVAAINMGGGITYYADSVKGRFTISQDNAKNTVYLLMNSLEPEDTAIYYCAADSTIYASYYECGHGLSTGGYGYDSWGQGTQVTVSSRR 135
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain B from PDB  Type:PROTEIN  Length:133
                                                                                                                                                                     
               SCOP domains d1jtpb_ B: Camelid IG heavy chain variable domain, VHh                                                                                SCOP domains
               CATH domains 1jtpB00 B:1-133 Immunoglobulins                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.eeee....eeeeeeee.......eeeeeee......eeeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeeeee.........hhhhhhh......ee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jtp B   1 DVQLQASGGGSVQAGGSLRLSCAASGYTIGPYCMGWFRQAPGKEREGVAAINMGGGITYYADSVKGRFTISQDNAKNTVYLLMNSLEPEDTAIYYCAADSTIYASYYECGHGLSTGGYGYDSWGQGTQVTVSS 133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain L from PDB  Type:PROTEIN  Length:129
 aligned with LYSC_MELGA | P00703 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:129
                                    28        38        48        58        68        78        88        98       108       118       128       138         
           LYSC_MELGA    19 KVYGRCELAAAMKRLGLDNYRGYSLGNWVCAAKFESNFNTHATNRNTDGSTDYGILQINSRWWCNDGRTPGSKNLCNIPCSALLSSDITASVNCAKKIASGGNGMNAWVAWRNRCKGTDVHAWIRGCRL 147
               SCOP domains d1jtpl_ L: Lysozyme                                                                                                               SCOP domains
               CATH domains 1jtpL00 L:1-129  [code=1.10.530.10, no name defined]                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....eee.....eee....ee...................hhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhhhhh...hhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) LACTALBUMIN_LYSOZYME_2  PDB: L:1-129 UniProt: 19-147                                                                              PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------LACTALBUMIN_LYSOZYM----------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jtp L   1 KVYGRCELAAAMKRLGLDNYRGYSLGNWVCAAKFESNFNTHATNRNTDGSTDYGILQINSRWWCNDGRTPGSKNLCNIPCSALLSSDITASVNCAKKIASGGNGMNAWVAWRNRCKGTDVHAWIRGCRL 129
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain M from PDB  Type:PROTEIN  Length:129
 aligned with LYSC_MELGA | P00703 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:129
                                    28        38        48        58        68        78        88        98       108       118       128       138         
           LYSC_MELGA    19 KVYGRCELAAAMKRLGLDNYRGYSLGNWVCAAKFESNFNTHATNRNTDGSTDYGILQINSRWWCNDGRTPGSKNLCNIPCSALLSSDITASVNCAKKIASGGNGMNAWVAWRNRCKGTDVHAWIRGCRL 147
               SCOP domains d1jtpm_ M: Lysozyme                                                                                                               SCOP domains
               CATH domains 1jtpM00 M:1-129  [code=1.10.530.10, no name defined]                                                                              CATH domains
           Pfam domains (1) Lys-1jtpM01 M:1-127                                                                                                            -- Pfam domains (1)
           Pfam domains (2) Lys-1jtpM02 M:1-127                                                                                                            -- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....eee.....eee....ee...................hhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) LACTALBUMIN_LYSOZYME_2  PDB: M:1-129 UniProt: 19-147                                                                              PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------LACTALBUMIN_LYSOZYM----------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jtp M   1 KVYGRCELAAAMKRLGLDNYRGYSLGNWVCAAKFESNFNTHATNRNTDGSTDYGILQINSRWWCNDGRTPGSKNLCNIPCSALLSSDITASVNCAKKIASGGNGMNAWVAWRNRCKGTDVHAWIRGCRL 129
                                    10        20        30        40        50        60        70        80        90       100       110       120

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Lysozyme (1131)

Homologous Superfamily: [code=1.10.530.10, no name defined] (605)

Arabian camel (Camelus dromedarius) (10)

1a	1jtpL00	L:1-129
1b	1jtpM00	M:1-129

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Arabian camel (Camelus dromedarius) (15)

2a	1jtpB00	B:1-133
2b	1jtpA00	A:1-135

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Lysozyme (266)

Family: Lys (245)

Meleagris gallopavo (Common turkey) (9)

1a	Lys-1jtpM01	M:1-127
1b	Lys-1jtpM02	M:1-127

Asymmetric Unit(hide GO term definitions)

Chain L,M (LYSC_MELGA | P00703)

molecular function
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0016798	hydrolase activity, acting on glycosyl bonds	Catalysis of the hydrolysis of any glycosyl bond.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0003796	lysozyme activity	Catalysis of the hydrolysis of the beta-(1->4) linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan.
biological process
	GO:0019835	cytolysis	The rupture of cell membranes and the loss of cytoplasm.
	GO:0042742	defense response to bacterium	Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0001895	retina homeostasis	A tissue homeostatic process involved in the maintenance of an internal equilibrium within the retina of the eye, including control of cellular proliferation and death and control of metabolic function.
cellular component
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

Asymmetric Unit
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		Gly B:30 - Pro B:31	[ RasMol ]

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	1jtp
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	LYSC_MELGA \| P00703	:	135l 1dzb 1jef 1jse 1ljn 1lz2 1lzy 1tew 1uac 1xft 2lz2 3lz2

1jto	1JTO IS A RE-REFINED VERSION OF 1MEL WHICH IS ISOMOROPHOUS AND CONTAINS THE SAME ANTIBODY. THE LYSOZYME MOLECULES ARE FROM DIFFERENT SPECIES
1mel	THIS STRUCTURE IS ISOMOROPHOUS AND CONTAINS THE SAME ANTIBODY. THE LYSOZYME MOLECULES ARE FROM DIFFERENT SPECIES

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