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(-) Description

Title :  THREE-DIMENSIONAL STRUCTURE OF A HUMAN IMMUNOGLOBULIN WITH A HINGE DELETION
 
Authors :  L. W. Guddat, A. B. Edmundson
Date :  25 Feb 93  (Deposition) - 31 Jan 94  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  H,L
Biol. Unit 1:  H,L  (2x)
Keywords :  Immunoglobulin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. W. Guddat, J. N. Herron, A. B. Edmundson
Three-Dimensional Structure Of A Human Immunoglobulin With Hinge Deletion.
Proc. Natl. Acad. Sci. Usa V. 90 4271 1993
PubMed-ID: 8483943  |  Reference-DOI: 10.1073/PNAS.90.9.4271
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - IGG1 MCG INTACT ANTIBODY (LIGHT CHAIN)
    Chains: L
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - IGG1 MCG INTACT ANTIBODY (HEAVY CHAIN)
    Chains: H
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : HL
Biological Unit 1 (2x): HL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 10)

Asymmetric Unit (7, 10)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2FUL1Ligand/IonBETA-L-FUCOSE
3GAL1Ligand/IonBETA-D-GALACTOSE
4GUP1Ligand/IonALPHA-L-GULOPYRANOSIDE
5MAN1Ligand/IonALPHA-D-MANNOSE
6NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
7SIA1Ligand/IonO-SIALIC ACID
Biological Unit 1 (7, 20)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2FUL2Ligand/IonBETA-L-FUCOSE
3GAL2Ligand/IonBETA-D-GALACTOSE
4GUP2Ligand/IonALPHA-L-GULOPYRANOSIDE
5MAN2Ligand/IonALPHA-D-MANNOSE
6NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
7SIA2Ligand/IonO-SIALIC ACID

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP H:250 , ASN H:282 , SER H:283 , THR H:284 , FUL H:430 , NAG H:431BINDING SITE FOR RESIDUE NAG H 429
02AC2SOFTWARETYR H:281 , ASN H:282 , NAG H:429BINDING SITE FOR RESIDUE FUL H 430
03AC3SOFTWAREVAL H:249 , ASP H:250 , NAG H:429 , BMA H:432 , MAN H:433 , GUP H:437BINDING SITE FOR RESIDUE NAG H 431
04AC4SOFTWAREPHE H:226 , PHE H:228 , VAL H:249 , NAG H:431 , MAN H:433 , GUP H:437 , NAG H:438BINDING SITE FOR RESIDUE BMA H 432
05AC5SOFTWAREPHE H:228 , ARG H:286 , NAG H:431 , BMA H:432 , NAG H:434BINDING SITE FOR RESIDUE MAN H 433
06AC6SOFTWAREPHE H:228 , THR H:245 , VAL H:247 , ARG H:286 , VAL H:288 , MAN H:433 , GAL H:435BINDING SITE FOR RESIDUE NAG H 434
07AC7SOFTWAREPRO H:229 , GLU H:243 , THR H:245 , VAL H:288 , NAG H:434 , SIA H:436BINDING SITE FOR RESIDUE GAL H 435
08AC8SOFTWARETHR H:241 , PRO H:242 , GLU H:243 , THR H:245 , VAL H:290 , LEU H:291 , THR H:292 , GAL H:435BINDING SITE FOR RESIDUE SIA H 436
09AC9SOFTWARESER H:224 , VAL H:225 , PHE H:226 , LYS H:319 , NAG H:431 , BMA H:432 , NAG H:438BINDING SITE FOR RESIDUE GUP H 437
10BC1SOFTWAREPHE H:226 , LYS H:319 , BMA H:432 , GUP H:437BINDING SITE FOR RESIDUE NAG H 438
11HC1AUTHORTHR H:31 , ILE H:32 , LEU H:33 , TYR H:34 , TYR H:35 , TRP H:36 , SER H:37ANTIGEN COMBINING SITE 1 IN CHAIN H
12HC2AUTHORTYR H:52 , ILE H:53 , TYR H:54 , TYR H:55 , SER H:56 , GLY H:57 , SER H:58 , THR H:59 , TYR H:60 , GLY H:61 , ASN H:62 , PRO H:63 , SER H:64 , LEU H:65ANTIGEN COMBINING SITE 2 IN CHAIN H
13HC3AUTHORVAL H:100 , PRO H:101 , LEU H:102 , VAL H:103 , VAL H:104 , ASN H:105 , PRO H:106ANTIGEN COMBINING SITE 3 IN CHAIN H
14LC1AUTHORTHR L:23 , GLY L:24 , THR L:25 , SER L:26 , SER L:27 , ASP L:28 , VAL L:29 , GLY L:30 , GLY L:31 , TYR L:32 , ASN L:33 , TYR L:34 , VAL L:35 , SER L:36ANTIGEN COMBINING SITE 1 IN CHAIN L
15LC2AUTHORGLU L:52 , VAL L:53 , ASN L:54 , LYS L:55 , ARG L:56 , PRO L:57 , SER L:58ANTIGEN COMBINING SITE 2 IN CHAIN L
16LC3AUTHORSER L:91 , SER L:92 , TYR L:93 , GLU L:94 , GLY L:95 , SER L:96 , ASP L:97 , ASN L:98 , PHE L:99 , VAL L:100ANTIGEN COMBINING SITE 3 IN CHAIN L

(-) SS Bonds  (7, 7)

Asymmetric Unit
No.Residues
1H:22 -H:97
2H:144 -H:200
3H:246 -H:306
4H:352 -H:410
5L:22 -L:90
6L:138 -L:197
7L:215 -L:215

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1MCO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1MCO)

(-) 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 H from PDB  Type:PROTEIN  Length:428
                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains d1mcoh1 H:1-117 Immunoglobulin heavy chain variable domain, VH                                                       d1mcoh2 H:118-219 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                       d1mcoh3 H:220-327 Immunoglobulin heavy chain gamma constant domain 2, CH2-gamma                             d1mcoh4 H:328-428 Immunoglobulin heavy chain gamma constant domain 3, CH3-gamma                       SCOP domains
               CATH domains 1mcoH01 H:1-118 Immunoglobulins                                                                                       -1mcoH02 H:120-221 Immunoglobulins                                                                     -1mcoH03 H:223-326 Immunoglobulins                                                                       -1mcoH04 H:328-428 Immunoglobulins                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) ...eeeeeeeeee...eeeeeeeee.......eeeeeeeeeeeeeeeeeeeeeeeeeeeeeee...eeeeeeeee.eeeeeeeee......eeeeeeeeeeeeeeeeeeeeeeeeee.....eeeeeee.........eeeeeeeeeee....eeeeeeeee..eeeeeeeeeeee.eeeeeeeeeeee......eeeeeeeeee..eeeeeee........eeeeeee.hhhhhhh...eeeeeeeeee.......eeeeeeeeeeeee...eeeeeeeeeeeeeeeeeeeeehhhhhh.eeeeeeeee.....eeeeeee.....-----------hhhhh----------------..eeeeeeeeeeeeeeeeeeeeeeee.-----------hhhhhh...eeeeeeee......eeeeeee. Sec.struct. author (1)
     Sec.struct. author (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee---------------------------eeeeeeeeeeeeee---------------------------- Sec.struct. author (2)
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mco H   1 PLVLQESGPGLVKPSEALSLTCTVSGDSINTILYYWSWIRQPPGKGLEWIGYIYYSGSTYGNPSLKSRVTISVNTSKNQFYSKLSSVTAADTAVYYCARVPLVVNPWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPQPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPQVKFNWYVDGVQVHNAKTKPREQQYNSTYRVVSVLTVLHQNWLDGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSL 428
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420        


Chain L from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains d1mcol1 L:1-111 Immunoglobulin light chain lambda variable domain, VL-lambda                                   d1mcol2 L:112-216 Immunoglobulin light chain lambda constant domain, CL-lambda                            SCOP domains
               CATH domains 1mcoL01 L:1-111 Immunoglobulins                                                                                1mcoL02 L:112-212 Immunoglobulins                                                                    ---- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
     Sec.struct. author (1) ...eeeeeeeeee...eeeeeeee........eeeeeeeeeeeeeeeeeeeeeeee.......eeeeeeeeeeeeeee......eeeeeeeeeee..eeeeeeeeeeeeee.....--------hhhhhh..eeeeeeeee......eeeeeeeee....eeeeeee.........eeeeeeeehhhhhhhheeeeeeeeeeeeeeeee....... Sec.struct. author (1)
     Sec.struct. author (2) --------------------------------------------------------------------------------------------------------------------eeeeeeeee------------------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1mco L   1 PSALTQPPSASGSLGQSVTISCTGTSSDVGGYNYVSWYQQHAGKAPKVIIYEVNKRPSGVPDRFSGSKSGNTASLTVSGLQAEDEADYYCSSYEGSDNFVFGTGTKVTVLGQPKANPTVTLFPPSSEELQANKATEVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS 216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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  (6, 6)

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

(-) CATH Domains  (1, 6)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)
(-)
Architecture: Sandwich (5577)
(-)
Topology: Immunoglobulin-like (3897)
(-)
Homologous Superfamily: Immunoglobulins (2282)
(-)
Human (Homo sapiens) (912)
1a1mcoH02H:120-221
1b1mcoH04H:328-428
1c1mcoL01L:1-111
1d1mcoH01H:1-118
1e1mcoL02L:112-212
1f1mcoH03H:223-326

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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