SCOPe 2.08: Protein: Peptide deformylase

Lineage for Protein: Peptide deformylase

Root: SCOPe 2.08
Class d: Alpha and beta proteins (a+b) [53931] (396 folds)
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
Superfamily d.167.1: Peptide deformylase [56420] (2 families)
nickel-dependent enzyme
Family d.167.1.1: Peptide deformylase [56421] (2 proteins)
automatically mapped to Pfam PF01327
Protein Peptide deformylase [56422] (11 species)

Species:

Bacillus stearothermophilus [TaxId:1422] [75580] (1 PDB entry)
- Domain for 1lqy:
  - Domain d1lqya_: 1lqy A: [74212]
    complexed with antibiotic actinonin
    complexed with bb2, ni
Enterococcus faecalis [TaxId:1351] [225419] (2 PDB entries)
1. Domain for 2os0:
  - Domain d2os0a1: 2os0 A:1-187 [205356]
    Other proteins in same PDB: d2os0a2
    automated match to d1vezb_
    complexed with ni, so4
2. Domain for 2os1:
  - Domain d2os1a1: 2os1 A:1-187 [205357]
    Other proteins in same PDB: d2os1a2
    automated match to d1vezb_
    complexed with bb2, ni, so4
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:
  - Domain d1bsja_: 1bsj A: [42302]
    complexed with co, mln, po4
7. Domain for 1bsk:
  - Domain d1bska_: 1bsk A: [42303]
    complexed with mln, po4, zn
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:
  - Domain d1defa_: 1def A: [42306]
    incorrect model(?)
    complexed with zn
10. Domain for 1dff:
  - Domain d1dffa_: 1dff A: [42304]
    complexed with zn
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:
  - Domain d1xema_: 1xem A: [121911]
    automated match to d1bs4a_
    complexed with fmt, zn
16. Domain for 1xen:
  - Domain d1xena_: 1xen A: [121912]
    automated match to d1bs4a_
    complexed with fe, fmt
17. Domain for 1xeo:
  - Domain d1xeoa_: 1xeo A: [121913]
    automated match to d1bs4a_
    complexed with co, fmt
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:
  - Domain d2defa_: 2def A: [42305]
    complexed with ni
20. Domain for 2kmn:
  - Domain d2kmna_: 2kmn A: [242567]
    automated match to d1defa_
    complexed with bb2, zn
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
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
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
Pneumococcus (Streptococcus pneumoniae) [TaxId:1313] [90057] (10 PDB entries)
1. Domain for 1lm6:
  - Domain d1lm6a_: 1lm6 A: [84628]
    complexed with fe, gol
2. Domain for 2ai7:
  - Domain d2ai7a_: 2ai7 A: [162816]
    automated match to d1lm6a_
    complexed with ni, sb7, so4
3. Domain for 2aia:
  - Domain d2aiaa_: 2aia A: [162817]
    automated match to d1lm6a_
    complexed with ni, sb8, so4
4. Domain for 2aie:
  - Domain d2aiep_: 2aie P: [162818]
    automated match to d1lm6a_
    complexed with ni, sb9, so4
5. Domain for 3str:
  - Domain d3strp_: 3str P: [185561]
    automated match to d1lm6a_
    complexed with 3li, gol, ni, so4
6. Domain for 3svj:
  - Domain d3svjp_: 3svj P: [185562]
    automated match to d1lm6a_
    complexed with 4li, gol, ni, so4
7. Domain for 3sw8:
  - Domain d3sw8p_: 3sw8 P: [185568]
    automated match to d1lm6a_
    complexed with 5li, ni, so4
8. Domain for 4eox:
  - Domain d4eoxp_: 4eox P: [195281]
    automated match to d1lm6a_
    complexed with 0s5, ni
9. Domain for 6ow2:
  - Domain d6ow2p_: 6ow2 P: [371205]
    automated match to d3svjp_
    complexed with nb4, ni
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
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
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:
  - Domain d1lmha_: 1lmh A: [74036]
    complexed with zn
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:
  - Domain d1q1ya1: 1q1y A:1-183 [104480]
    Other proteins in same PDB: d1q1ya2
    complexed with bb2, zn
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:
  - Domain d6jfga_: 6jfg A: [380355]
    automated match to d1lqwa_
    complexed with k1u, ni
7. Domain for 6jfq:
  - Domain d6jfqa_: 6jfq A: [380410]
    automated match to d1lmha_
    complexed with k2u, ni
8. Domain for 6jfr:
  - Domain d6jfra_: 6jfr A: [380370]
    automated match to d1lqwa_
    complexed with k3u, ni
9. Domain for 6jfs:
  - Domain d6jfsa_: 6jfs A: [380375]
    automated match to d1lqwa_
    complexed with lhy, ni
Streptococcus pyogenes [TaxId:160490] [188359] (1 PDB entry)
- Domain for 2os3:
  - Domain d2os3a1: 2os3 A:2-204 [166836]
    Other proteins in same PDB: d2os3a2
    automated match to d1lm6a_
    complexed with bb2, co
Thermotoga maritima [TaxId:2336] [90058] (1 PDB entry)
- Domains for 1lme:
  1. Domain d1lmea1: 1lme A:1-145 [84629]
    Other proteins in same PDB: d1lmea2, d1lmeb2
  2. Domain d1lmeb1: 1lme B:1-145 [84630]
    Other proteins in same PDB: d1lmea2, d1lmeb2
Thermus thermophilus [TaxId:274] [118165] (1 PDB entry)
Uniprot P43522
- Domains for 1v3y:
  1. Domain d1v3ya_: 1v3y A: [113508]
  2. Domain d1v3yb_: 1v3y B: [113509]

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:

Protein Peptide deformylase from d.167.1.1: Peptide deformylase first appeared (with stable ids) in SCOP 1.55
Protein Peptide deformylase from d.167.1.1: Peptide deformylase appears in SCOPe 2.07