Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) 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) - 25 Aug 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B,P
Keywords :  Immunoglobulin, Immune System (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-L-GLN-D-PHE-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  (4, 4)

Asymmetric/Biological Unit (4, 4)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2DPN1Mod. Amino AcidD-PHENYLALANINE
3DPR1Mod. Amino AcidD-PROLINE
4NH21Mod. Amino AcidAMINO GROUP

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
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
04BC1AUTHORTHR 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
05BC2AUTHORILE B:50 , TYR B:51 , GLU B:52 , VAL B:53 , ASN B:54 , LYS B:55PEPTIDE BINDING SITE 2 IN CHAIN B
06BC3AUTHORSER 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
07SC1SOFTWAREPHE A:99 , TYR B:38 , VAL B:48 , GLN P:1BINDING SITE FOR RESIDUE ACE P 0
08SC2SOFTWARETYR B:34 , VAL B:35 , SER B:36 , GLU B:52 , TYR B:93 , GLN P:1 , HIS P:3 , DPR P:4BINDING SITE FOR RESIDUE DPN P 2
09SC3SOFTWARETYR A:34 , TYR B:34 , TYR B:93 , DPN P:2 , HIS P:3 , NH2 P:5BINDING SITE FOR RESIDUE DPR P 4
10SC4SOFTWARETYR B:34 , DPR P:4BINDING SITE FOR RESIDUE NH2 P 5

(-) 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 1MCC)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1MCC)

(-) 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:216
                                                                                                                                                                                                                                                        
               SCOP domains d1mcca1 A:1-111 Immunoglobulin light chain lambda variable domain, VL-lambda                                   d1mcca2 A:112-216 Immunoglobulin light chain lambda constant domain, CL-lambda                            SCOP domains
               CATH domains 1mccA01 A:1-111 Immunoglobulins                                                                                1mccA02 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
                 1mcc A   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 B from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains d1mccb1 B:1-111 Immunoglobulin light chain lambda variable domain, VL-lambda                                   d1mccb2 B:112-216 Immunoglobulin light chain lambda constant domain, CL-lambda                            SCOP domains
               CATH domains 1mccB01 B:1-111 Immunoglobulins                                                                                1mccB02 B:112-212 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
                 1mcc 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:6
                                      
               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
                 1mcc P   0 xQxHxx   5
                            | | ||
                            0-ACE|
                              2-DPN
                                4-DPR
                                 5-NH2
   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 1MCC)

(-) Gene Ontology  (0, 0)

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

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    ACE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    DPN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    DPR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NH2  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    SC1  [ RasMol ]  +environment [ RasMol ]
    SC2  [ RasMol ]  +environment [ RasMol ]
    SC3  [ RasMol ]  +environment [ RasMol ]
    SC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Tyr A:144 - Pro A:145   [ RasMol ]  
    Tyr B:144 - Pro B:145   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1mcc
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  (no 'UniProt ID/Accession number' available) |
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  (no 'UniProt ID/Accession number' available) |
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

(no "Entries Sharing at Least One Protein Chain" available for 1MCC)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1MCC)