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(-) Description

Title :  CRYSTAL STRUCTURE OF FOUR-HELIX BUNDLE MODEL
 
Authors :  L. Di Costanzo, S. Geremia
Date :  17 Jul 01  (Deposition) - 16 Jan 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Keywords :  Alpha-Helical Bundle, Protein Design, De Novo Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Di Costanzo, H. Wade, S. Geremia, L. Randaccio, V. Pavone, W. F. Degrado, A. Lombardi
Toward The De Novo Design Of A Catalytically Active Helix Bundle: A Substrate-Accessible Carboxylate-Bridged Dinuclear Metal Center.
J. Am. Chem. Soc. V. 123 12749 2001
PubMed-ID: 11749531  |  Reference-DOI: 10.1021/JA010506X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (FOUR-HELIX BUNDLE MODEL)
    ChainsA, B, C, D, E, F
    EngineeredYES
    Other DetailsTHIS PROTEIN WAS CHEMICALLY SYNTHESIZED
    SyntheticYES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)AB    
Biological Unit 2 (1x)  CD  
Biological Unit 3 (1x)    EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 26)

Asymmetric Unit (4, 26)
No.NameCountTypeFull Name
1ACE6Mod. Amino AcidACETYL GROUP
2DMS3Ligand/IonDIMETHYL SULFOXIDE
3MN11Ligand/IonMANGANESE (II) ION
4NH26Mod. Amino AcidAMINO GROUP
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
2DMS1Ligand/IonDIMETHYL SULFOXIDE
3MN-1Ligand/IonMANGANESE (II) ION
4NH22Mod. Amino AcidAMINO GROUP
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
2DMS1Ligand/IonDIMETHYL SULFOXIDE
3MN-1Ligand/IonMANGANESE (II) ION
4NH22Mod. Amino AcidAMINO GROUP
Biological Unit 3 (3, 5)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
2DMS1Ligand/IonDIMETHYL SULFOXIDE
3MN-1Ligand/IonMANGANESE (II) ION
4NH22Mod. Amino AcidAMINO GROUP

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:10 , GLU A:36 , HIS A:39 , GLU B:36 , DMS B:301 , MN B:402BINDING SITE FOR RESIDUE MN A 401
02AC2SOFTWAREGLU A:36 , MN A:401 , GLU B:10 , GLU B:36 , HIS B:39 , DMS B:301BINDING SITE FOR RESIDUE MN B 402
03AC3SOFTWAREGLU C:10 , GLU C:36 , HIS C:39 , DMS C:302 , GLU D:36 , MN D:404BINDING SITE FOR RESIDUE MN C 403
04AC4SOFTWAREGLU C:36 , DMS C:302 , MN C:403 , GLU D:10 , GLU D:36 , HIS D:39BINDING SITE FOR RESIDUE MN D 404
05AC5SOFTWAREGLU E:10 , GLU E:36 , HIS E:39 , GLU F:36 , DMS F:303BINDING SITE FOR RESIDUE MN E 405
06AC6SOFTWAREGLU E:36 , GLU F:10 , GLU F:36 , HIS F:39 , DMS F:303BINDING SITE FOR RESIDUE MN F 406
07AC7SOFTWAREHOH C:506 , GLN D:16 , GLU D:19 , HOH D:505 , GLU F:34 , HOH F:407BINDING SITE FOR RESIDUE MN D 501
08AC8SOFTWAREGLU B:37 , HOH B:504 , GLU E:34 , GLU E:37 , HOH E:503BINDING SITE FOR RESIDUE MN E 502
09AC9SOFTWAREGLN B:16 , GLU B:19 , HOH B:505 , HOH B:506 , HOH B:507BINDING SITE FOR RESIDUE MN B 503
10BC1SOFTWAREGLU D:34 , GLU D:37 , HOH D:506 , HOH D:507 , HOH D:508BINDING SITE FOR RESIDUE MN D 504
11BC2SOFTWAREGLU A:37 , GLN C:16 , GLU C:19 , HOH C:507 , HOH C:508BINDING SITE FOR RESIDUE MN C 505
12BC3SOFTWARELEU A:9 , GLU A:10 , ALA A:13 , GLU A:36 , MN A:401 , LEU B:9 , GLU B:10 , ALA B:13 , GLU B:36 , MN B:402BINDING SITE FOR RESIDUE DMS B 301
13BC4SOFTWARELEU C:9 , GLU C:10 , ALA C:13 , GLU C:36 , MN C:403 , GLU D:10 , ALA D:13 , GLU D:36 , MN D:404BINDING SITE FOR RESIDUE DMS C 302
14BC5SOFTWAREGLU E:10 , GLU E:36 , MN E:405 , LEU F:9 , GLU F:10 , ALA F:13 , GLU F:36 , MN F:406BINDING SITE FOR RESIDUE DMS F 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1JM0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1JM0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1JM0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1JM0)

(-) Exons   (0, 0)

(no "Exon" information available for 1JM0)

(-) 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:50
                                                                                 
               SCOP domains d1jm0a_ A: Artificial diiron protein               SCOP domains
               CATH domains -1jm0A00 A:1-48 Immunoglobulin FC, subunit C     - CATH domains
               Pfam domains -------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------- Transcript
                  1jm0 A  0 xDYLRELLKLELQAIKQYREALEYVKLPVLAKILEDEEKHIEWLETILGx 49
                            |        9        19        29        39        49
                            |                                               49-NH2
                            0-ACE                                             

Chain B from PDB  Type:PROTEIN  Length:50
                                                                                 
               SCOP domains d1jm0b_ B: Artificial diiron protein               SCOP domains
               CATH domains -1jm0B00 B:1-48 Immunoglobulin FC, subunit C     - CATH domains
               Pfam domains -------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------- Transcript
                  1jm0 B  0 xDYLRELLKLELQAIKQYREALEYVKLPVLAKILEDEEKHIEWLETILGx 49
                            |        9        19        29        39        49
                            |                                               49-NH2
                            0-ACE                                             

Chain C from PDB  Type:PROTEIN  Length:50
                                                                                 
               SCOP domains d1jm0c_ C: Artificial diiron protein               SCOP domains
               CATH domains -1jm0C00 C:1-48 Immunoglobulin FC, subunit C     - CATH domains
               Pfam domains -------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------- Transcript
                  1jm0 C  0 xDYLRELLKLELQAIKQYREALEYVKLPVLAKILEDEEKHIEWLETILGx 49
                            |        9        19        29        39        49
                            |                                               49-NH2
                            0-ACE                                             

Chain D from PDB  Type:PROTEIN  Length:50
                                                                                 
               SCOP domains d1jm0d_ D: Artificial diiron protein               SCOP domains
               CATH domains -1jm0D00 D:1-48 Immunoglobulin FC, subunit C     - CATH domains
               Pfam domains -------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------- Transcript
                  1jm0 D  0 xDYLRELLKLELQAIKQYREALEYVKLPVLAKILEDEEKHIEWLETILGx 49
                            |        9        19        29        39        49
                            |                                               49-NH2
                            0-ACE                                             

Chain E from PDB  Type:PROTEIN  Length:50
                                                                                 
               SCOP domains d1jm0e_ E: Artificial diiron protein               SCOP domains
               CATH domains -1jm0E00 E:1-48 Immunoglobulin FC, subunit C     - CATH domains
               Pfam domains -------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------- Transcript
                  1jm0 E  0 xDYLRELLKLELQAIKQYREALEYVKLPVLAKILEDEEKHIEWLETILGx 49
                            |        9        19        29        39        49
                            |                                               49-NH2
                            0-ACE                                             

Chain F from PDB  Type:PROTEIN  Length:50
                                                                                 
               SCOP domains d1jm0f_ F: Artificial diiron protein               SCOP domains
               CATH domains -1jm0F00 F:1-48 Immunoglobulin FC, subunit C     - CATH domains
               Pfam domains -------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------- Transcript
                  1jm0 F  0 xDYLRELLKLELQAIKQYREALEYVKLPVLAKILEDEEKHIEWLETILGx 49
                            |        9        19        29        39        49
                            |                                               49-NH2
                            0-ACE                                             

   Legend:   → Mismatch (orange background)
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    → 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  (1, 6)

Asymmetric Unit

(-) CATH Domains  (1, 6)

Asymmetric Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1JM0)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1JM0)

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 Related Entries

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

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(-) Related Entries Specified in the PDB File

1ec5 1EC5 IS THE ZINC DERIVATIVE WITH ALA13 RESIDUE MUTATED TO LEU
1jmb 1JMB IS A DIFFERENT CRYSTALLINE FORM (S.G. C 2 2 21) OF THE SAME STRUCTURE