Lineage for Protein: Peptide deformylase

  1. Root: SCOPe 2.08
  2. Class d: Alpha and beta proteins (a+b) [53931] (396 folds)
  3. Fold d.167: Peptide deformylase [56419] (1 superfamily)
    alpha-beta(5)-alpha; 3 layers: a/b/a; meander beta-sheet wraps around the C-terminal alpha-helix
  4. Superfamily d.167.1: Peptide deformylase [56420] (2 families) (S)
    nickel-dependent enzyme
  5. Family d.167.1.1: Peptide deformylase [56421] (2 proteins)
    automatically mapped to Pfam PF01327
  6. Protein Peptide deformylase [56422] (11 species)

Species:

  1. Bacillus stearothermophilus [TaxId:1422] [75580] (1 PDB entry)
    • Domain for 1lqy:
      • Domain d1lqya_: 1lqy A: [74212]
        complexed with antibiotic actinonin
        complexed with bb2, ni
  2. Enterococcus faecalis [TaxId:1351] [225419] (2 PDB entries)
    1. Domain for 2os0:
    2. Domain for 2os1:
  3. Escherichia coli [TaxId:562] [56423] (21 PDB entries)
    1. Domains for 1bs4:
      1. Domain d1bs4a_: 1bs4 A: [42287]
        complexed with 2pe, so4, zn
      2. Domain d1bs4b_: 1bs4 B: [42288]
        complexed with 2pe, so4, zn
      3. Domain d1bs4c_: 1bs4 C: [42289]
        complexed with 2pe, so4, zn
    2. Domains for 1bs5:
      1. Domain d1bs5a_: 1bs5 A: [42296]
        complexed with so4, zn
      2. Domain d1bs5b_: 1bs5 B: [42297]
        complexed with so4, zn
      3. Domain d1bs5c_: 1bs5 C: [42298]
        complexed with so4, zn
    3. Domains for 1bs6:
      1. Domain d1bs6a_: 1bs6 A: [42290]
        complexed with ni, so4
      2. Domain d1bs6b_: 1bs6 B: [42291]
        complexed with ni, so4
      3. Domain d1bs6c_: 1bs6 C: [42292]
        complexed with ni, so4
    4. Domains for 1bs7:
      1. Domain d1bs7a_: 1bs7 A: [42299]
        complexed with ni, so4
      2. Domain d1bs7b_: 1bs7 B: [42300]
        complexed with ni, so4
      3. Domain d1bs7c_: 1bs7 C: [42301]
        complexed with ni, so4
    5. Domains for 1bs8:
      1. Domain d1bs8a_: 1bs8 A: [42293]
        complexed with so4, zn
      2. Domain d1bs8b_: 1bs8 B: [42294]
        complexed with so4, zn
      3. Domain d1bs8c_: 1bs8 C: [42295]
        complexed with so4, zn
    6. Domain for 1bsj:
    7. Domain for 1bsk:
    8. Domains for 1bsz:
      1. Domain d1bsza_: 1bsz A: [42281]
        complexed with 2pe, fe, so4
      2. Domain d1bszb_: 1bsz B: [42282]
        complexed with 2pe, fe, so4
      3. Domain d1bszc_: 1bsz C: [42283]
        complexed with 2pe, fe, so4
    9. Domain for 1def:
    10. Domain for 1dff:
    11. Domains for 1g27:
      1. Domain d1g27a_: 1g27 A: [65106]
        complexed with bb1, ni
      2. Domain d1g27b_: 1g27 B: [65107]
        complexed with bb1, ni
      3. Domain d1g27c_: 1g27 C: [65108]
        complexed with bb1, ni
    12. Domains for 1g2a:
      1. Domain d1g2aa_: 1g2a A: [65109]
        complexed with bb2, ni
      2. Domain d1g2ab_: 1g2a B: [65110]
        complexed with bb2, ni
      3. Domain d1g2ac_: 1g2a C: [65111]
        complexed with bb2, ni
    13. Domains for 1icj:
      1. Domain d1icja_: 1icj A: [42284]
        complexed with 2pe, ni, so4
      2. Domain d1icjb_: 1icj B: [42285]
        complexed with 2pe, ni, so4
      3. Domain d1icjc_: 1icj C: [42286]
        complexed with 2pe, ni, so4
    14. Domains for 1lru:
      1. Domain d1lrua_: 1lru A: [74228]
        complexed with antibiotic actinonin
        complexed with bb2, so4, zn
      2. Domain d1lrub_: 1lru B: [74229]
        complexed with antibiotic actinonin
        complexed with bb2, so4, zn
      3. Domain d1lruc_: 1lru C: [74230]
        complexed with antibiotic actinonin
        complexed with bb2, so4, zn
    15. Domain for 1xem:
    16. Domain for 1xen:
    17. Domain for 1xeo:
    18. Domains for 2ai8:
      1. Domain d2ai8a_: 2ai8 A: [126819]
        automated match to d1bs4a_
        complexed with ni, sb7
      2. Domain d2ai8b_: 2ai8 B: [126820]
        automated match to d1bs4a_
        complexed with ni, sb7
      3. Domain d2ai8c_: 2ai8 C: [126821]
        automated match to d1bs4a_
        complexed with ni, sb7
    19. Domain for 2def:
    20. Domain for 2kmn:
    21. Domains for 3k6l:
      1. Domain d3k6la_: 3k6l A: [179131]
        automated match to d1bs4a_
        complexed with 2bb, ni
      2. Domain d3k6lb_: 3k6l B: [179132]
        automated match to d1bs4a_
        complexed with 2bb, ni
      3. Domain d3k6lc_: 3k6l C: [179133]
        automated match to d1bs4a_
        complexed with 2bb, ni
  4. Leptospira interrogans [TaxId:173] [103340] (5 PDB entries)
    Uniprot Q72S74
    1. Domains for 1rn5:
      1. Domain d1rn5a_: 1rn5 A: [303023]
        automated match to d1y6ha_
        complexed with cbx, gly, zn
      2. Domain d1rn5b_: 1rn5 B: [303024]
        automated match to d1y6ha_
        complexed with cbx, gly, zn
    2. Domains for 1sv2:
      1. Domain d1sv2a_: 1sv2 A: [240765]
        automated match to d1y6ha_
        complexed with dtt, fmt, zn
      2. Domain d1sv2b_: 1sv2 B: [240766]
        automated match to d1y6ha_
        complexed with dtt, fmt, zn
    3. Domains for 1vev:
      1. Domain d1veva_: 1vev A: [161852]
        automated match to d1y6ha_
        complexed with fmt, mes, zn
      2. Domain d1vevb_: 1vev B: [161853]
        automated match to d1y6ha_
        complexed with fmt, mes, zn
    4. Domains for 1vez:
      1. Domain d1veza_: 1vez A: [161854]
        automated match to d1y6ha_
        complexed with fmt, trs, zn
      2. Domain d1vezb_: 1vez B: [161855]
        automated match to d1y6ha_
        complexed with fmt, trs, zn
    5. Domains for 1y6h:
      1. Domain d1y6ha_: 1y6h A: [116505]
        complexed with fmt, gly, zn
      2. Domain d1y6hb_: 1y6h B: [116506]
        complexed with fmt, gly, zn
  5. Malaria parasite (Plasmodium falciparum) [TaxId:5833] [75581] (3 PDB entries)
    1. Domains for 1jym:
      1. Domain d1jyma1: 1jym A:63-237 [71957]
        Other proteins in same PDB: d1jyma2, d1jymb2, d1jyme2
        complexed with co
      2. Domain d1jymb1: 1jym B:63-237 [71958]
        Other proteins in same PDB: d1jyma2, d1jymb2, d1jyme2
        complexed with co
      3. Domain d1jymc_: 1jym C: [71959]
        Other proteins in same PDB: d1jyma2, d1jymb2, d1jyme2
        complexed with co
      4. Domain d1jymd_: 1jym D: [71960]
        Other proteins in same PDB: d1jyma2, d1jymb2, d1jyme2
        complexed with co
      5. Domain d1jyme1: 1jym E:63-237 [71961]
        Other proteins in same PDB: d1jyma2, d1jymb2, d1jyme2
        complexed with co
      6. Domain d1jymf_: 1jym F: [71962]
        Other proteins in same PDB: d1jyma2, d1jymb2, d1jyme2
        complexed with co
      7. Domain d1jymg_: 1jym G: [71963]
        Other proteins in same PDB: d1jyma2, d1jymb2, d1jyme2
        complexed with co
      8. Domain d1jymh_: 1jym H: [71964]
        Other proteins in same PDB: d1jyma2, d1jymb2, d1jyme2
        complexed with co
      9. Domain d1jymi_: 1jym I: [71965]
        Other proteins in same PDB: d1jyma2, d1jymb2, d1jyme2
        complexed with co
      10. Domain d1jymj_: 1jym J: [71966]
        Other proteins in same PDB: d1jyma2, d1jymb2, d1jyme2
        complexed with co
    2. Domains for 1rl4:
      1. Domain d1rl4a_: 1rl4 A: [97636]
        complexed with bl5, brr, co
      2. Domain d1rl4b_: 1rl4 B: [97637]
        complexed with bl5, brr, co
    3. Domains for 1rqc:
      1. Domain d1rqca1: 1rqc A:66-239 [97732]
        Other proteins in same PDB: d1rqca2, d1rqcb2, d1rqce2
        complexed with co
      2. Domain d1rqcb1: 1rqc B:66-239 [97733]
        Other proteins in same PDB: d1rqca2, d1rqcb2, d1rqce2
        complexed with co
      3. Domain d1rqcc_: 1rqc C: [97734]
        Other proteins in same PDB: d1rqca2, d1rqcb2, d1rqce2
        complexed with co
      4. Domain d1rqcd_: 1rqc D: [97735]
        Other proteins in same PDB: d1rqca2, d1rqcb2, d1rqce2
        complexed with co
      5. Domain d1rqce1: 1rqc E:66-239 [97736]
        Other proteins in same PDB: d1rqca2, d1rqcb2, d1rqce2
        complexed with co
      6. Domain d1rqcf_: 1rqc F: [97737]
        Other proteins in same PDB: d1rqca2, d1rqcb2, d1rqce2
        complexed with co
      7. Domain d1rqcg_: 1rqc G: [97738]
        Other proteins in same PDB: d1rqca2, d1rqcb2, d1rqce2
        complexed with co
      8. Domain d1rqch_: 1rqc H: [97739]
        Other proteins in same PDB: d1rqca2, d1rqcb2, d1rqce2
        complexed with co
      9. Domain d1rqci_: 1rqc I: [97740]
        Other proteins in same PDB: d1rqca2, d1rqcb2, d1rqce2
        complexed with co
      10. Domain d1rqcj_: 1rqc J: [97741]
        Other proteins in same PDB: d1rqca2, d1rqcb2, d1rqce2
        complexed with co
  6. Pneumococcus (Streptococcus pneumoniae) [TaxId:1313] [90057] (10 PDB entries)
    1. Domain for 1lm6:
    2. Domain for 2ai7:
    3. Domain for 2aia:
    4. Domain for 2aie:
    5. Domain for 3str:
    6. Domain for 3svj:
    7. Domain for 3sw8:
    8. Domain for 4eox:
    9. Domain for 6ow2:
    10. Domains for 6ow7:
      1. Domain d6ow7p_: 6ow7 P: [371223]
        automated match to d3svjp_
        complexed with n9y, ni, so4
      2. Domain d6ow7q_: 6ow7 Q: [371222]
        automated match to d3svjp_
        complexed with n9y, ni, so4
  7. Pseudomonas aeruginosa [TaxId:287] [75578] (4 PDB entries)
    1. Domains for 1ix1:
      1. Domain d1ix1a1: 1ix1 A:2-168 [90712]
        Other proteins in same PDB: d1ix1a2, d1ix1b2
        complexed with antibiotic actinonin
        complexed with bb2, mha, zn
      2. Domain d1ix1b1: 1ix1 B:2-168 [90713]
        Other proteins in same PDB: d1ix1a2, d1ix1b2
        complexed with antibiotic actinonin
        complexed with bb2, mha, zn
    2. Domain for 1lry:
      • Domain d1lrya_: 1lry A: [74231]
        complexed with antibiotic actinonin
        complexed with bb2, zn
    3. Domains for 1n5n:
      1. Domain d1n5na_: 1n5n A: [85336]
        complexed with gol, zn
      2. Domain d1n5nb_: 1n5n B: [85337]
        complexed with gol, zn
    4. Domains for 1s17:
      1. Domain d1s17a_: 1s17 A: [98335]
        complexed with gnr, gol, ni
      2. Domain d1s17b_: 1s17 B: [98336]
        complexed with gnr, gol, ni
  8. Staphylococcus aureus [TaxId:1280] [75579] (9 PDB entries)
    Uniprot Q9F4L4
    1. Domains for 1lm4:
      1. Domain d1lm4a1: 1lm4 A:1-183 [84626]
        Other proteins in same PDB: d1lm4a2, d1lm4b2
        complexed with fe, gol
      2. Domain d1lm4b1: 1lm4 B:1-183 [84627]
        Other proteins in same PDB: d1lm4a2, d1lm4b2
        complexed with fe, gol
    2. Domain for 1lmh:
    3. Domains for 1lqw:
      1. Domain d1lqwa_: 1lqw A: [74210]
        complexed with zn
      2. Domain d1lqwb_: 1lqw B: [74211]
        complexed with zn
    4. Domain for 1q1y:
    5. Domains for 2ai9:
      1. Domain d2ai9a_: 2ai9 A: [126822]
        automated match to d1lqwa_
        complexed with ni, so4
      2. Domain d2ai9b_: 2ai9 B: [126823]
        automated match to d1lqwa_
        complexed with ni, so4
    6. Domain for 6jfg:
    7. Domain for 6jfq:
    8. Domain for 6jfr:
    9. Domain for 6jfs:
  9. Streptococcus pyogenes [TaxId:160490] [188359] (1 PDB entry)
  10. Thermotoga maritima [TaxId:2336] [90058] (1 PDB entry)
  11. Thermus thermophilus [TaxId:274] [118165] (1 PDB entry)
    Uniprot P43522

More info for Protein Peptide deformylase from d.167.1.1: Peptide deformylase

Timeline for Protein Peptide deformylase from d.167.1.1: Peptide deformylase: