1NC2 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF MONOCLONAL ANTIBODY 2D12.5 FAB COMPLEXED WITH Y-DOTA

Authors :   T. M. Corneillie, A. J. Fisher, C. F. Meares

Date :   04 Dec 02 (Deposition) - 16 Dec 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Antibody-Dota Complex, Rare Earth, Dota, Metal Chelate, Yttrium, Gamma Turn, N-Linked Glycosylation, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. M. Corneillie, A. J. Fisher, C. F. Meares
Crystal Structures Of Two Complexes Of The Rare-Earth-Dota-Binding Antibody 2D12. 5: Ligand Generality From A Chiral System.
J. Am. Chem. Soc. V. 125 15039 2003
PubMed-ID: 14653738 | Reference-DOI: 10.1021/JA037236Y

Molecule 1 - MONOCLONAL ANTIBODY 2D12.5, LAMBDA LIGHT CHAIN
	Cell Line	:	MYELOMA LINE PX63 AG8 FUSED WITH ANTIBODY EXPRESSING SPLEEN CELLS
	Chains	:	A, C
	Fragment	:	FAB
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Strain	:	BALB/C

Molecule 2 - MONOCLONAL ANTIBODY 2D12.5, IGG1 GAMMA HEAVY CHAIN
	Cell Line	:	MYELOMA LINE PX63 AG8 FUSED WITH ANTIBODY EXPRESSING SPLEEN CELLS
	Chains	:	B
	Fragment	:	FAB
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Strain	:	BALB/C

Molecule 3 - MONOCLONAL ANTIBODY 2D12.5, IGG1 GAMMA HEAVY CHAIN
	Cell Line	:	MYELOMA LINE PX63 AG8 FUSED WITH ANTIBODY EXPRESSING SPLEEN CELLS
	Chains	:	D
	Fragment	:	FAB
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Strain	:	BALB/C

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 8)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	DOE	2	Ligand/Ion	(S)-2-(4-(2-(2-HYDROXYETHYLTHIO)-ACETAMIDO)-BENZYL)-1,4,7,10-TETRAAZACYCLODODECANE-N,N',N'',N'''-TETRAACETATE
3	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID
5	YT3	2	Ligand/Ion	YTTRIUM (III) ION

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	DOE	1	Ligand/Ion	(S)-2-(4-(2-(2-HYDROXYETHYLTHIO)-ACETAMIDO)-BENZYL)-1,4,7,10-TETRAAZACYCLODODECANE-N,N',N'',N'''-TETRAACETATE
3	NAG	-1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID
5	YT3	1	Ligand/Ion	YTTRIUM (III) ION

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	DOE	1	Ligand/Ion	(S)-2-(4-(2-(2-HYDROXYETHYLTHIO)-ACETAMIDO)-BENZYL)-1,4,7,10-TETRAAZACYCLODODECANE-N,N',N'',N'''-TETRAACETATE
3	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	PCA	-1	Mod. Amino Acid	PYROGLUTAMIC ACID
5	YT3	1	Ligand/Ion	YTTRIUM (III) ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL C:146 , GLU C:201 , ASN D:88 , HOH D:601	BINDING SITE FOR RESIDUE NAG D 400
2	AC2	SOFTWARE	DOE B:500 , HOH B:506	BINDING SITE FOR RESIDUE YT3 B 502
3	AC3	SOFTWARE	DOE D:501 , HOH D:509	BINDING SITE FOR RESIDUE YT3 D 503
4	AC4	SOFTWARE	HOH A:520	BINDING SITE FOR RESIDUE CL A 504
5	AC5	SOFTWARE	DOE D:501	BINDING SITE FOR RESIDUE CL C 505
6	AC6	SOFTWARE	TYR A:34 , THR A:82 , TRP A:93 , TRP A:98 , GLN A:111 , PRO A:112 , TRP B:52 , ARG B:98 , SER B:100 , TYR B:101 , ASN B:104 , YT3 B:502 , HOH B:504 , HOH B:506 , HOH B:509 , HOH B:531 , HOH B:532	BINDING SITE FOR RESIDUE DOE B 500
7	AC7	SOFTWARE	ALA A:35 , TRP A:37 , GLY A:52 , ASN A:53 , ASN A:54 , SER A:67 , ALA A:73 , ALA A:74 , HOH A:577 , HOH A:578 , TYR C:34 , TRP C:93 , TRP C:98 , CL C:505 , TRP D:52 , ARG D:98 , SER D:100 , TYR D:101 , ASN D:104 , YT3 D:503 , HOH D:504 , HOH D:505 , HOH D:506 , HOH D:509 , HOH D:546	BINDING SITE FOR RESIDUE DOE D 501

Asymmetric Unit

No.	Residues
1	A:22	-	A:90
2	A:137	-	A:196
3	B:22	-	B:95
4	B:146	-	B:201
5	C:22	-	C:90
6	C:137	-	C:196
7	C:214	-	D:221
8	D:22	-	D:95
9	D:146	-	D:201

Asymmetric Unit

No.	Residues
1	Tyr A:143	-	Pro A:144
2	Tyr B:101	-	Pro B:102
3	Phe B:152	-	Pro B:153
4	Glu B:154	-	Pro B:155
5	Trp B:194	-	Pro B:195
6	Tyr C:143	-	Pro C:144
7	Tyr D:101	-	Pro D:102
8	Phe D:152	-	Pro D:153
9	Glu D:154	-	Pro D:155
10	Trp D:194	-	Pro D:195

(no "SAP(SNP)/Variant" information available for 1NC2)

(no "PROSITE Motif" information available for 1NC2)

(no "Exon" information available for 1NC2)

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:211
                                                                                                                                                                                                                                                   
               SCOP domains d1nc2a1 A:1-110 Immunoglobulin light chain lambda variable domain, VL-lambda                                  d1nc2a2 A:111-211 Immunoglobulin light chain lambda constant domain, CL-lambda                        SCOP domains
               CATH domains 1nc2A01 A:1-110 Immunoglobulins                                                                               1nc2A02 A:111-210 Immunoglobulins                                                                   - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee..eeee....eeeeeeee.....hhhhh.eeeeee...eeeeee.............eeeeee..eeeeeee..hhhhheeeeeeee....eee...eeeee........eeeee....hhhhh.eeeeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeeeeehhhhhhh..eeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nc2 A   1 QAVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPDHLFTGLIGGNNNRPPGVPARFSGSLIGDKAALTIAGTQTEDEAIYFCALWYSNHWVFGGGTRLTVLGQPKSSPSVTLFPPSSEELETNKATLVCTITDFYPGVVTVDWKVDGTPVTQGMETTQPSKQSNNKYMASSYLTLTARAWERHSSYSCQVTHEGHTVEKSLSP 211
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain B from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains d1nc2b1 B:1-120 Immunoglobulin heavy chain variable domain, VH                                                          d1nc2b2 B:121-219 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                     SCOP domains
               CATH domains -1nc2B01 B:2-119 Immunoglobulins                                                                                       1nc2B02 B:120-218 Immunoglobulins                                                                  - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee.......eeeeeee.....eeeeeee.....eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeee..............eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee....eeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nc2 B   1 xVKLQESGPGLVQPSQSLSITCTVSGFSLTDYGVHWVRQSPGKGLEWLGVIWSGGGTAYTAAFISRLNIYKDNSKNQVFFEMNSLQANDTAMYYCARRGSYPYNYFDVWGQGTTVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR 219
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         
                            1-PCA

Chain C from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains d1nc2c1 C:1-110 Immunoglobulin light chain lambda variable domain, VL-lambda                                  d1nc2c2 C:111-215 Immunoglobulin light chain lambda constant domain, CL-lambda                            SCOP domains
               CATH domains 1nc2C01 C:1-110 Immunoglobulins                                                                               1nc2C02 C:111-210 Immunoglobulins                                                                   ----- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee..eeee.....eeeeeee.....hhhhh.eeeeee...eeeeee.............eeeeee..eeeeee...hhhhheeeeeeee....eee...eeeee........eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeeeeehhhhhhh..eeeeeee..eeeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nc2 C   1 QAVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPDHLFTGLIGGNNNRPPGVPARFSGSLIGDKAALTIAGTQTEDEAIYFCALWYSNHWVFGGGTRLTVLGQPKSSPSVTLFPPSSEELETNKATLVCTITDFYPGVVTVDWKVDGTPVTQGMETTQPSKQSNNKYMASSYLTLTARAWERHSSYSCQVTHEGHTVEKSLSPAECS 215
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain D from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains d1nc2d1 D:1-120 Immunoglobulin heavy chain variable domain, VH                                                          d1nc2d2 D:121-221 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                 SCOP domains
               CATH domains 1nc2D01 D:1-119 Immunoglobulins                                                                                        1nc2D02 D:120-218 Immunoglobulins                                                            --- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....ee.....eeeeeeee......eeeeeeee.....eeeeeee.....eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeeee.............eeeee........eeeee....eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nc2 D   1 QVKLQESGPGLVQPSQSLSITCTVSGFSLTDYGVHWVRQSPGKGLEWLGVIWSGGGTAYTAAFISRLNIYKDNSKNQVFFEMNSLQANDTAMYYCARRGSYPYNYFDVWGQGTTVTVSSAKTTPPSVYPLAPGSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDC 221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  ||   146       156       166       176       186       196       206       216     
                                                                                                                                                              133|                                                                                 
                                                                                                                                                               140

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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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

House mouse (Mus musculus) (616)

1a	1nc2B02	B:120-218
1b	1nc2D02	D:120-218
1c	1nc2A01	A:1-110
1d	1nc2C01	C:1-110
1e	1nc2B01	B:2-119
1f	1nc2D01	D:1-119
1g	1nc2A02	A:111-210
1h	1nc2C02	C:111-210

(no "Pfam Domain" information available for 1NC2)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 1NC2)

Asymmetric Unit
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	Cis Peptide Bonds
		Glu B:154 - Pro B:155	[ RasMol ]
		Glu D:154 - Pro D:155	[ RasMol ]
		Phe B:152 - Pro B:153	[ RasMol ]
		Phe D:152 - Pro D:153	[ RasMol ]
		Trp B:194 - Pro B:195	[ RasMol ]
		Trp D:194 - Pro D:195	[ RasMol ]
		Tyr A:143 - Pro A:144	[ RasMol ]
		Tyr B:101 - Pro B:102	[ RasMol ]
		Tyr C:143 - Pro C:144	[ RasMol ]
		Tyr D:101 - Pro D:102	[ RasMol ]

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	1nc2
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1nc4	MONOCLONAL ANTIBODY 2D12.5 FAB COMPLEXED WITH GD-DOTA

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 8)

Sites (7, 7)

SS Bonds (9, 9)

Cis Peptide Bonds (10, 10)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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SCOP Domains (4, 8)

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