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(-) Description

Title :  CRYSTAL STRUCTURE OF MONOCLONAL ANTIBODY 2D12.5 FAB COMPLEXED WITH GD-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 :  2.25
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, Gadolinium, 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

(-) Compounds

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

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 8)

Asymmetric Unit (5, 8)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2DOF2Ligand/Ion(S)-2-(4-NITROBENZYL)-1,4,7,10-TETRAAZACYCLODODECANE-N,N',N'',N'''-TETRAACETATE
3GD32Ligand/IonGADOLINIUM ION
4NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
5PCA1Mod. Amino AcidPYROGLUTAMIC ACID
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2DOF1Ligand/Ion(S)-2-(4-NITROBENZYL)-1,4,7,10-TETRAAZACYCLODODECANE-N,N',N'',N'''-TETRAACETATE
3GD31Ligand/IonGADOLINIUM ION
4NAG-1Ligand/IonN-ACETYL-D-GLUCOSAMINE
5PCA1Mod. Amino AcidPYROGLUTAMIC ACID
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2DOF1Ligand/Ion(S)-2-(4-NITROBENZYL)-1,4,7,10-TETRAAZACYCLODODECANE-N,N',N'',N'''-TETRAACETATE
3GD31Ligand/IonGADOLINIUM ION
4NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
5PCA-1Mod. Amino AcidPYROGLUTAMIC ACID

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL C:146 , GLU C:201 , ASN D:88BINDING SITE FOR RESIDUE NAG D 400
2AC2SOFTWAREHOH A:560BINDING SITE FOR RESIDUE CL A 504
3AC3SOFTWARETYR A:34 , TRP A:93 , TRP A:98 , TRP B:52 , ARG B:98 , SER B:100 , TYR B:101 , ASN B:104 , GD3 B:502 , HOH B:512 , HOH B:513 , HOH B:515 , HOH B:524 , HOH B:525 , DOF D:501BINDING SITE FOR RESIDUE DOF B 500
4AC4SOFTWARETHR A:159 , TYR B:101 , DOF B:500 , TYR C:34 , TRP C:93 , TRP C:98 , TRP D:52 , ARG D:98 , SER D:100 , TYR D:101 , ASN D:104 , GD3 D:503 , HOH D:504 , HOH D:505 , HOH D:506 , HOH D:515 , HOH D:549BINDING SITE FOR RESIDUE DOF D 501
5AC5SOFTWAREDOF B:500 , HOH B:513BINDING SITE FOR RESIDUE GD3 B 502
6AC6SOFTWAREDOF D:501 , HOH D:505BINDING SITE FOR RESIDUE GD3 D 503

(-) SS Bonds  (8, 8)

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

(-) Cis Peptide Bonds  (10, 10)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1NC4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1NC4)

(-) Exons   (0, 0)

(no "Exon" information available for 1NC4)

(-) Sequences/Alignments

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 d1nc4a1 A:1-110 Immunoglobulin light chain lambda variable domain, VL-lambda                                  d1nc4a2 A:111-211 Immunoglobulin light chain lambda constant domain, CL-lambda                        SCOP domains
               CATH domains 1nc4A01 A:1-110 Immunoglobulins                                                                               1nc4A02 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..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeeeeehhhhhhh..eeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nc4 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 d1nc4b1 B:1-120 Immunoglobulin heavy chain variable domain, VH                                                          d1nc4b2 B:121-219 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                     SCOP domains
               CATH domains -1nc4B01 B:2-119 Immunoglobulins                                                                                       1nc4B02 B:120-218 Immunoglobulins                                                                  - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.......eeeeeee.....eeeeeee.....eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeee..............eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee....eeeeeeeeee.........eeeeee....eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nc4 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 d1nc4c1 C:1-110 Immunoglobulin light chain lambda variable domain, VL-lambda                                  d1nc4c2 C:111-215 Immunoglobulin light chain lambda constant domain, CL-lambda                            SCOP domains
               CATH domains 1nc4C01 C:1-110 Immunoglobulins                                                                               1nc4C02 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
                 1nc4 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 d1nc4d1 D:1-120 Immunoglobulin heavy chain variable domain, VH                                                          d1nc4d2 D:121-220 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                 SCOP domains
               CATH domains 1nc4D01 D:1-119 Immunoglobulins                                                                                        1nc4D02 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
                 1nc4 D   1 QVKLQESGPGLVQPSQSLSITCTVSGFSLTDYGVHWVRQSPGKGLEWLGVIWSGGGTAYTAAFISRLNIYKDNSKNQVFFEMNSLQANDTAMYYCARRGSYPYNYFDVWGQGTTVTVSSAKTTPPSVYPLAPGSSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRD 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   ||  145       155       165       175       185       195       205       215     
                                                                                                                                                               134|                                                                                
                                                                                                                                                                140
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (4, 8)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 8)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)
(-)
Architecture: Sandwich (5577)
(-)
Topology: Immunoglobulin-like (3897)
(-)
Homologous Superfamily: Immunoglobulins (2282)
(-)
House mouse (Mus musculus) (616)
1a1nc4B02B:120-218
1b1nc4D02D:120-218
1c1nc4A01A:1-110
1d1nc4C01C:1-110
1e1nc4D01D:1-119
1f1nc4B01B:2-119
1g1nc4A02A:111-210
1h1nc4C02C:111-210

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1NC4)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1NC4)

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 Related Entries

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(-) Related Entries Specified in the PDB File

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