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(-) Description

Title :  STRUCTURES OF A MONOCLONAL ANTI-ICAM-1 ANTIBODY R6.5 FRAGMENT AT 2.8 ANGSTROMS RESOLUTION
 
Authors :  M. J. Jedrzejas, M. Luo
Date :  16 Dec 94  (Deposition) - 27 Feb 95  (Release) - 25 Aug 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Immunoglobulin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. J. Jedrzejas, J. Miglietta, J. A. Griffin, M. Luo
Structure Of A Monoclonal Anti-Icam-1 Antibody R6. 5 Fab Fragment At 2. 8 A Resolution.
Acta Crystallogr. , Sect. D V. 51 380 1995
PubMed-ID: 15299305  |  Reference-DOI: 10.1107/S0907444994011054
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - IGG2A-KAPPA R6.5 FAB (LIGHT CHAIN)
    Chains: L
    Engineered: YES
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - IGG2A-KAPPA R6.5 FAB (HEAVY CHAIN)
    Chains: H
    Engineered: YES
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : HL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1RMF)

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1CH1AUTHORASP H:31 , TYR H:32 , ALA H:33 , ILE H:34 , HIS H:35COMPLEMENTARITY DETERMINING REGION FOR HEAVY CHAIN, 1
2CH2AUTHORVAL H:50 , ILE H:51 , SER H:52 , ALA H:53 , TYR H:54 , SER H:55 , GLY H:56 , ASP H:57 , THR H:58 , ASN H:59 , TYR H:60 , ASN H:61 , GLN H:62 , LYS H:63 , PHE H:64 , LYS H:65 , GLY H:66COMPLEMENTARITY DETERMINING REGION FOR HEAVY CHAIN, 2
3CH3AUTHORGLY H:99 , GLY H:100 , TRP H:101 , LEU H:102 , LEU H:103 , LEU H:104 , SER H:105 , PHE H:106 , ASP H:107 , TYR H:108COMPLEMENTARITY DETERMINING REGION FOR HEAVY CHAIN, 3
4CL1AUTHORARG L:24 , SER L:25 , SER L:26 , GLN L:27 , SER L:28 , LEU L:29 , VAL L:30 , HIS L:31 , SER L:32 , ASN L:33 , GLY L:34 , ASN L:35 , ASN L:36 , TYR L:37 , LEU L:38 , HIS L:39COMPLEMENTARITY DETERMINING REGION FOR LIGHT CHAIN, 1
5CL2AUTHORLYS L:55 , VAL L:56 , SER L:57 , ASN L:58 , ARG L:59 , PHE L:60 , SER L:61COMPLEMENTARITY DETERMINING REGION FOR LIGHT CHAIN, 2
6CL3AUTHORSER L:94 , GLN L:95 , SER L:96 , THR L:97 , HIS L:98 , VAL L:99 , PRO L:100 , LEU L:101 , THR L:102COMPLEMENTARITY DETERMINING REGION FOR LIGHT CHAIN, 3

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:96
2L:139 -L:199

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Ser L:7 -Pro L:8
2Val L:99 -Pro L:100
3Tyr L:145 -Pro L:146
4Gly H:8 -Pro H:9
5Phe H:152 -Pro H:153
6Glu H:154 -Pro H:155

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1RMF)

(-) Sequences/Alignments

Asymmetric/Biological 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:216
                                                                                                                                                                                                                                                        
               SCOP domains d1rmfh1 H:1-119 Immunoglobulin heavy chain variable domain, VH                                                         d1rmfh2 H:120-216 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                   SCOP domains
               CATH domains 1rmfH01 H:1-119 Immunoglobulins                                                                                        1rmfH02 H:120-216 Immunoglobulins                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee..eee....eeeeeeeee...hhh..eeeeee.....eeeeeee..........hhh...eeee..hhh.eeeeeee...hhh..eeeeee................eee........eeeee..........eeeeeeeeeee.....eeeehhh.....eee...eeee.eeeeeeeeeeehhh.......eeee............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1rmf H   1 QVQLQQSGPELVRPGVSVKISCKGSGYTFIDYAIHWVKESHAKSLEWIGVISAYSGDTNYNQKFKGKATMTVDKSSNTAYLELARLTSEDSAIYYCARGGWLLLSFDYWGQGTTLTVSSAKTTAPSVTPLAPVCGDTTGSSVTLGVLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKI 216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210      


Chain L from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains d1rmfl1 L:1-112 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1rmfl2 L:113-219 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1rmfL01 L:1-113 Immunoglobulins                                                                                  1rmfL02 L:114-217 Immunoglobulins                                                                       -- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee............eeeeee......eeeeee...........eeeeee..eeeeee....hhh..eeeeee............eeee.......eeeee...hhhh...eeeeeeeeeee.....eeeeee........eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rmf L   1 DVVMTQSPLSLPVSLGDQASISCRSSQSLVHSNGNNYLHWYLQKSGQAPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQSTHVPLTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 219
                                    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)
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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 '|'

 Classification and Annotation

(-) SCOP Domains  (4, 4)

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

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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  Cis Peptide Bonds
    Glu H:154 - Pro H:155   [ RasMol ]  
    Gly H:8 - Pro H:9   [ RasMol ]  
    Phe H:152 - Pro H:153   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
    Tyr L:145 - Pro L:146   [ RasMol ]  
    Val L:99 - Pro L:100   [ RasMol ]  
 

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