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(-) Description

Title :  PRINCIPLES AND PITFALLS IN DESIGNING SITE DIRECTED PEPTIDE LIGANDS
 
Authors :  A. B. Edmundson, D. L. Harris, Z. -C. Fan, L. W. Guddat
Date :  25 Feb 93  (Deposition) - 31 Jan 94  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B,P
Keywords :  Immunoglobulin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. B. Edmundson, D. L. Harris, Z. C. Fan, L. W. Guddat, B. T. Schley, B. L. Hanson, G. Tribbick, H. M. Geysen
Principles And Pitfalls In Designing Site-Directed Peptide Ligands.
Proteins V. 16 246 1993
PubMed-ID: 8346191  |  Reference-DOI: 10.1002/PROT.340160304
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - IMMUNOGLOBULIN LAMBDA DIMER MCG (LIGHT CHAIN)
    Chains: A, B
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - PEPTIDE N-ACETYL-D-PHE-B-ALA-L-HIS-D-PRO-NH2
    Chains: P
    Engineered: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 6)

Asymmetric/Biological Unit (6, 6)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2BAL1Mod. Amino AcidBETA-ALANINE
3DPN1Ligand/IonD-PHENYLALANINE
4DPR1Ligand/IonD-PROLINE
5HIS1Mod. Amino AcidHISTIDINE
6NH21Mod. ResidueAMINO GROUP

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1AUTHORTHR A:23 , GLY A:24 , THR A:25 , SER A:26 , SER A:27 , ASP A:28 , VAL A:29 , GLY A:30 , GLY A:31 , TYR A:32 , ASN A:33 , TYR A:34 , VAL A:35 , SER A:36PEPTIDE BINDING SITE 1 IN CHAIN A
02AC2AUTHORILE A:50 , TYR A:51 , GLU A:52 , VAL A:53 , ASN A:54 , LYS A:55PEPTIDE BINDING SITE 2 IN CHAIN A
03AC3AUTHORSER A:91 , SER A:92 , TYR A:93 , GLU A:94 , GLY A:95 , SER A:96 , ASP A:97 , ASN A:98 , PHE A:99 , VAL A:100PEPTIDE BINDING SITE 3 IN CHAIN A
04AC4SOFTWAREPHE A:99 , THR A:108 , TYR B:34 , BAL P:2 , DPN P:7 , DPR P:8BINDING SITE FOR RESIDUE HIS P 6
05AC5SOFTWARETYR A:38 , PHE A:99 , PHE B:99 , DPN P:7BINDING SITE FOR RESIDUE ACE A 0
06AC6SOFTWAREACE A:0 , PHE A:99 , TYR B:34 , SER B:36 , GLU B:52 , PHE B:99 , BAL P:2 , HIS P:6BINDING SITE FOR RESIDUE DPN P 7
07AC7SOFTWARETYR A:93 , ASP A:97 , NH2 A:217 , HIS P:6BINDING SITE FOR RESIDUE DPR P 8
08AC8SOFTWAREPRO A:145 , DPR P:8BINDING SITE FOR RESIDUE NH2 A 217
09BC1AUTHORTHR B:23 , GLY B:24 , THR B:25 , SER B:26 , SER B:27 , ASP B:28 , VAL B:29 , GLY B:30 , GLY B:31 , TYR B:32 , ASN B:33 , TYR B:34 , VAL B:35 , SER B:36PEPTIDE BINDING SITE 1 IN CHAIN B
10BC2AUTHORILE B:50 , TYR B:51 , GLU B:52 , VAL B:53 , ASN B:54 , LYS B:55PEPTIDE BINDING SITE 2 IN CHAIN B
11BC3AUTHORSER B:91 , SER B:92 , TYR B:93 , GLU B:94 , GLY B:95 , SER B:96 , ASP B:97 , ASN B:98 , PHE B:99 , VAL B:100PEPTIDE BINDING SITE 3 IN CHAIN B

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:22 -A:90
2A:138 -A:197
3A:215 -B:215
4B:22 -B:90
5B:138 -B:197

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:144 -Pro A:145
2Tyr B:144 -Pro B:145

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1MCD)

(-) 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 A from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains d1mcda1 A:1-111 Immunoglobulin light chain lambda variable domain, VL-lambda                                   d1mcda2 A:112-216 Immunoglobulin light chain lambda constant domain, CL-lambda                           - SCOP domains
               CATH domains 1mcdA01 A:1-111 Immunoglobulins                                                                                1mcdA02 A:112-212 Immunoglobulins                                                                    ----- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeeeeee..........eeeeee......eeeeeee.........eeeeeee.eeeeeeeeeehh...eeeeeeeeee..eeeeeeeeeeeee....eeeeeeee..hhhhhhhh.eeeeeeeeeee....eeeeeee......eeeeeeeeee..eeeeeeeeeeehhhhhhhh.eeeeeeee..eeeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mcd A   1 PSALTQPPSASGSLGQSVTISCTGTSSDVGGYNYVSWYQQHAGKAPKVIIYEVNKRPSGVPDRFSGSKSGNTASLTVSGLQAEDEADYYCSSYEGSDNFVFGTGTKVTVLGQPKANPTVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECSx   0
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210     ||
                                                                                                                                                                                                                                                 216|
                                                                                                                                                                                                                                                    0-ACE


Chain B from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains d1mcdb1 B:1-111 Immunoglobulin light chain lambda variable domain, VL-lambda                                   d1mcdb2 B:112-216 Immunoglobulin light chain lambda constant domain, CL-lambda                            SCOP domains
               CATH domains 1mcdB01 B:1-111 Immunoglobulins                                                                                1mcdB02 B:112-216 Immunoglobulins                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..............eeeeeeeeee..........eeeeee......eeeeeee.........eeeeeee.eeeeeeeeeehh...eeeeeee.......eeeeeeeeeee....eeeeeeee..hhhhhhhh.eeeeeeeeeee....eeeeeee........eeeeeeee..eeeeeeeeeeehhhhhhh..eeeeeeee..eeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1mcd B   1 PSALTQPPSASGSLGQSVTISCTGTSSDVGGYNYVSWYQQHAGKAPKVIIYEVNKRPSGVPDRFSGSKSGNTASLTVSGLQAEDEADYYCSSYEGSDNFVFGTGTKVTVLGQPKANPTVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS 216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210      


Chain P from PDB  Type:PROTEIN  Length:2
                                  
               SCOP domains -- SCOP domains
               CATH domains -- CATH domains
               Pfam domains -- Pfam domains
         Sec.struct. author .. Sec.struct. author
                 SAPs(SNPs) -- SAPs(SNPs)
                    PROSITE -- PROSITE
                 Transcript -- Transcript
                 1mcd P   2 aH   6
                            ||
                            2-BAL
                             6
   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  (2, 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 1MCD)

(-) Gene Ontology  (0, 0)

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

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