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(-) Description

Title :  CORKSCREW ASSEMBLY OF SOD1 RESIDUES 28-38
 
Authors :  S. Sangwan, A. Zhao, M. R. Sawaya, D. Eisenberg
Date :  05 Sep 15  (Deposition) - 14 Sep 16  (Release) - 14 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H
Keywords :  Amyloid-Related Oligomer, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Sangwan, D. Eisenberg, M. R. Sawaya, A. Zhao, K. L. Adams, C. Jayson, A. B. Soriaga, E. Guenther, B. G. Novitch, C. Koehler
The Corkscrew: The Atomic Structure Of A Cylindrin-Related, Cytotoxic Oligomer Of Sod1
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SUPEROXIDE DISMUTASE [CU-ZN]
    Chains: A, B, C, D, E, F, G, H
    EC Number: 1.15.1.1
    Engineered: YES
    Fragment: RESIDUES 29-39
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: SYNTHESIZED
    Synonym: SUPEROXIDE DISMUTASE 1,HSOD1
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric/Biological Unit : ABCDEFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2IOD2Ligand/IonIODIDE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:28 , LYS A:30 , LYS B:28 , GLY H:33 , SER H:34 , HOH H:102binding site for residue GOL B 101
2AC2SOFTWARELYS D:30 , TRP G:32 , LYS H:30binding site for residue IOD D 101
3AC3SOFTWARETRP D:32 , LYS E:30 , LYS F:28 , SER G:34binding site for residue IOD D 102

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DLI)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5DLI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DLI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DLI)

(-) Exons   (0, 0)

(no "Exon" information available for 5DLI)

(-) 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:11
                                          
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author .eeeee..... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                  5dli A 28 KVKVWGSIKGL 38
                                    37 


Chain B from PDB  Type:PROTEIN  Length:11
                                          
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author .eeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                  5dli B 28 KVKVWGSIKGL 38
                                    37 


Chain C from PDB  Type:PROTEIN  Length:11
                                          
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author .eeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                  5dli C 28 KVKVWGSIKGL 38
                                    37 


Chain D from PDB  Type:PROTEIN  Length:11
                                          
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author .eeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                  5dli D 28 KVKVWGSIKGL 38
                                    37 


Chain E from PDB  Type:PROTEIN  Length:11
                                          
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author .eeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                  5dli E 28 KVKVWGSIKGL 38
                                    37 


Chain F from PDB  Type:PROTEIN  Length:11
                                          
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author .eeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                  5dli F 28 KVKVWGSIKGL 38
                                    37 


Chain G from PDB  Type:PROTEIN  Length:11
                                          
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author .eeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                  5dli G 28 KVKVWGSIKGL 38
                                    37 


Chain H from PDB  Type:PROTEIN  Length:11
                                          
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author .eeeee..... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                  5dli H 28 KVKVWGSIKGL 38
                                    37
   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  (0, 0)

(no "SCOP Domain" information available for 5DLI)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DLI)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DLI)

(-) Gene Ontology  (100, 100)

Asymmetric/Biological Unit(hide GO term definitions)

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  5dli
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  SODC_HUMAN | P00441
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  1.15.1.1
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 Related Entries

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

UniProtKB/Swiss-Prot
        SODC_HUMAN | P00441: 1azv 1ba9 1dsw 1fun 1hl4 1hl5 1kmg 1l3n 1mfm 1n18 1n19 1oez 1ozt 1ozu 1p1v 1ptz 1pu0 1rk7 1sos 1spd 1uxl 1uxm 2af2 2c9s 2c9u 2c9v 2gbt 2gbu 2gbv 2lu5 2mp3 2nam 2nnx 2r27 2v0a 2vr6 2vr7 2vr8 2wko 2wyt 2wyz 2wz0 2wz5 2wz6 2xjk 2xjl 2zkw 2zkx 2zky 3cqp 3cqq 3ecu 3ecv 3ecw 3gqf 3gtv 3gzo 3gzp 3gzq 3h2p 3h2q 3hff 3k91 3kh3 3kh4 3ltv 3qqd 3re0 3t5w 4a7g 4a7q 4a7s 4a7t 4a7u 4a7v 4b3e 4bcy 4bcz 4bd4 4ff9 4mcm 4mcn 4nin 4nio 4nip 4oh2 4sod 4xcr 5iiw 5j07 5j0c 5j0f 5j0g 5k02 5u9m

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5DLI)