The FSSP File

The FSSP file is an output from the DALI program.

For every PDB file submitted to the ProKnow program, at least one FSSP file is needed.

If the PDB file has multiple domains, FSSP file for each domain need to be submitted.

Please submit your PDB file to the DALI Server and use the files obtained (the FSSP files) for input into the ProKnow program.

An example FSSP file

FSSP      FAMILIES OF STRUCTURALLY SIMILAR PROTEINS, VERSION 1.1 (Apr 1 1998)
CREATED   Mon Oct 29 20:31:27 GMT 2001 for dali on jura
METHOD    Dali ver. 2.0: Holm, L., Sander, C. (1993) J.Mol.Biol. 233,123-138
DATABASE  2860 protein chains
PDBID     1a0aA
HEADER    COMPLEX (TRANSCRIPTION FACTOR/DNA)
COMPND    phosphate system positive regulatory protein pho4 fragment (bhlh) biological_unit DNA fragment (uasp2(17))
SOURCE    (saccharomyces cerevisiae) baker's yeast
AUTHOR    T.Shimizu A.Toumoto K.Ihara M.Shimizu Y.Kyogoku N.Ogawa Y.Oshima T.Hakoshima
SEQLENGTH    63
NALIGN       10
WARNING   pairs with Z<2.0 are structurally dissimilar

## SUMMARY: PDB/chain identifiers and structural alignment statistics
NR. STRID1 STRID2  Z   RMSD LALI LSEQ2 %IDE REVERS PERMUT NFRAG TOPO PROTEIN
 1: 1a0aA  1a0aA  11.6  0.0   63    63  100      0      0     1 S    phosphate system positive regulatory protein pho4 fragm
 2: 1a0aA  1a0aB   5.1  2.4   60    63   82      0      0     4 S    phosphate system positive regulatory protein pho4 fragm
 3: 1a0aA  1am9A   3.6  2.5   53    80   25      0      0     4 S    sterol regulatory element binding protein 1a fragment (
 4: 1a0aA  1an2A   3.4  2.4   54    86   25      0      0     4 S    max protein fragment (myn protein) biological_unit DNA
 5: 1a0aA  1mdyA   2.9  3.2   51    68   14      0      0     5 S    Myod basic-helix-loop-helix (bhlh) domain (residues 102
 6: 1a0aA  2xat    2.9  2.1   38   208    3      0      0     5 S    xenobiotic acetyltransferase biological_unit
 7: 1a0aA  3pviA   2.5  4.3   48   156    7      0      0     4 S    pvuii endonuclease Mutant DNA (5'-d(TpGpApCpCpApGpCpTpG
 8: 1a0aA  1fgjA   2.3  4.0   55   499    0      0      0     5 S    hydroxylamine oxidoreductase
 9: 1a0aA  1an4A   2.2  4.7   52    65   20      0      0     4 S    usf fragment (upstream stimulatory factor 1) Mutant bio
10: 1a0aA  1qgrA   2.1  3.8   44   871    3      0      0     3 S    importin beta subunit (karyopherin beta-1, nuclear fact

OR
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Results

    * mol1A

DaliLite: Structural Neighbours
Query: mol1A MOLECULE: EPIDERMAL GROWTH FACTOR;
Matches are sorted by Z-score. Similarities with a Z-score lower than 2 are spurious.
Summary

  No:  Chain   Z    rmsd lali nres  %id  Description
   1:  1egf   12.7  0.0   53    53  100  EPIDERMAL GROWTH FACTOR (EGF) (NMR, 16 STRUCTURES)
   2:  3egf   10.6  1.0   53    53  100  EPIDERMAL GROWTH FACTOR (EGF) (NMR, 16 STRUCTURES AFTER
   3:  1mox-D  4.5  3.0   47    48   32   MOLECULE: EPIDERMAL GROWTH FACTOR RECEPTOR;
   4:  1ivo-C  4.3  2.7   44    47   61   MOLECULE: EPIDERMAL GROWTH FACTOR RECEPTOR;
   5:  1mox-C  4.2  3.1   47    49   30   MOLECULE: EPIDERMAL GROWTH FACTOR RECEPTOR;
   6:  1ivo-D  4.2  2.7   44    47   61   MOLECULE: EPIDERMAL GROWTH FACTOR RECEPTOR;
   7:  1jl9-A  4.1  2.2   41    42   71   MOLECULE: EPIDERMAL GROWTH FACTOR;
   8:  1xdt-R  3.9  2.0   40    41   33   MOLECULE: DIPHTHERIA TOXIN;