Current Protein Identity：P0A6K3
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Difference tags compare only the current result set; every original PDB and assembly record remains separate.
Related-Structure Differences
Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.
| PDB Entry | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Experimental Method | Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 1BS4 PEPTIDE DEFORMYLASE AS ZN2+ CONTAINING FORM (NATIVE) IN COMPLEX WITH INHIBITOR POLYETHYLENE GLYCOL Deposited 1998-09-01 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–168（168 aa）
|
Not recorded | ZN ZINC ION × 1 2PE NONAETHYLENE GLYCOL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 7.4；REFERENCE: D.GROCHE,A.BECKER,I.SCHLICHTING,W.KABSCH, S.SCHULTZ,A.F.V.WAGNER (
1998) BIOCHEM.BIOPHYS.RES.COMM. 246, 342, pH 7.4
|
Resolution 1.90 Å R-free 0.240 |
| 1BS4 PEPTIDE DEFORMYLASE AS ZN2+ CONTAINING FORM (NATIVE) IN COMPLEX WITH INHIBITOR POLYETHYLENE GLYCOL Deposited 1998-09-01 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–168（168 aa）
|
Not recorded | ZN ZINC ION × 1 2PE NONAETHYLENE GLYCOL × 1 SO4 SULFATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 7.4；REFERENCE: D.GROCHE,A.BECKER,I.SCHLICHTING,W.KABSCH, S.SCHULTZ,A.F.V.WAGNER (
1998) BIOCHEM.BIOPHYS.RES.COMM. 246, 342, pH 7.4
|
Resolution 1.90 Å R-free 0.240 |
| 1BS4 PEPTIDE DEFORMYLASE AS ZN2+ CONTAINING FORM (NATIVE) IN COMPLEX WITH INHIBITOR POLYETHYLENE GLYCOL Deposited 1998-09-01 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–168（168 aa）
|
Not recorded | ZN ZINC ION × 1 2PE NONAETHYLENE GLYCOL × 1 SO4 SULFATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 7.4；REFERENCE: D.GROCHE,A.BECKER,I.SCHLICHTING,W.KABSCH, S.SCHULTZ,A.F.V.WAGNER (
1998) BIOCHEM.BIOPHYS.RES.COMM. 246, 342, pH 7.4
|
Resolution 1.90 Å R-free 0.240 |
| 1BS5 PEPTIDE DEFORMYLASE AS ZN2+ CONTAINING FORM Deposited 1998-09-01 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–168（168 aa）
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 7.4；SEE: D.GROCHE,A.BECKER,I.SCHLICHTING,W.KABSCH, S.SCHULTZ,A.F.V.WAGNER (1998)
BIOCHEM.BIOPHYS.RES.COMM. 246, 342, pH 7.4
|
Resolution 2.50 Å R-free 0.258 |
| 1BS5 PEPTIDE DEFORMYLASE AS ZN2+ CONTAINING FORM Deposited 1998-09-01 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–168（168 aa）
|
Not recorded | ZN ZINC ION × 1 SO4 SULFATE ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 7.4；SEE: D.GROCHE,A.BECKER,I.SCHLICHTING,W.KABSCH, S.SCHULTZ,A.F.V.WAGNER (1998)
BIOCHEM.BIOPHYS.RES.COMM. 246, 342, pH 7.4
|
Resolution 2.50 Å R-free 0.258 |
| 1BS5 PEPTIDE DEFORMYLASE AS ZN2+ CONTAINING FORM Deposited 1998-09-01 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–168（168 aa）
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 7.4；SEE: D.GROCHE,A.BECKER,I.SCHLICHTING,W.KABSCH, S.SCHULTZ,A.F.V.WAGNER (1998)
BIOCHEM.BIOPHYS.RES.COMM. 246, 342, pH 7.4
|
Resolution 2.50 Å R-free 0.258 |
| 1BS6 PEPTIDE DEFORMYLASE AS NI2+ CONTAINING FORM IN COMPLEX WITH TRIPEPTIDE MET-ALA-SER Deposited 1998-09-01 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–168（168 aa）
|
Not recorded | NI NICKEL (II) ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 7.4；SEE: D.GROCHE,A.BECKER,I.SCHLICHTING,W.KABSCH, S.SCHULTZ,A.F.V.WAGNER (1998)
BIOCHEM.BIOPHYS.RES.COMM. 246, 342, pH 7.4
|
Resolution 2.10 Å R-free 0.258 |
| 1BS6 PEPTIDE DEFORMYLASE AS NI2+ CONTAINING FORM IN COMPLEX WITH TRIPEPTIDE MET-ALA-SER Deposited 1998-09-01 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–168（168 aa）
|
Not recorded | NI NICKEL (II) ION × 1 SO4 SULFATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 7.4；SEE: D.GROCHE,A.BECKER,I.SCHLICHTING,W.KABSCH, S.SCHULTZ,A.F.V.WAGNER (1998)
BIOCHEM.BIOPHYS.RES.COMM. 246, 342, pH 7.4
|
Resolution 2.10 Å R-free 0.258 |
| 1BS6 PEPTIDE DEFORMYLASE AS NI2+ CONTAINING FORM IN COMPLEX WITH TRIPEPTIDE MET-ALA-SER Deposited 1998-09-01 | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain C
1–168（168 aa）
|
Not recorded | NI NICKEL (II) ION × 1 SO4 SULFATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 7.4；SEE: D.GROCHE,A.BECKER,I.SCHLICHTING,W.KABSCH, S.SCHULTZ,A.F.V.WAGNER (1998)
BIOCHEM.BIOPHYS.RES.COMM. 246, 342, pH 7.4
|
Resolution 2.10 Å R-free 0.258 |
| 1BS7 PEPTIDE DEFORMYLASE AS NI2+ CONTAINING FORM Deposited 1998-09-01 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–168（168 aa）
|
Not recorded | NI NICKEL (II) ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 7.4；SEE: D.GROCHE,A.BECKER,I.SCHLICHTING,W.KABSCH, S.SCHULTZ,A.F.V.WAGNER (1998)
BIOCHEM.BIOPHYS.RES.COMM. 246, 342, pH 7.4
|
Resolution 2.50 Å R-free 0.272 |
| 1BS7 PEPTIDE DEFORMYLASE AS NI2+ CONTAINING FORM Deposited 1998-09-01 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–168（168 aa）
|
Not recorded | NI NICKEL (II) ION × 1 SO4 SULFATE ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 7.4；SEE: D.GROCHE,A.BECKER,I.SCHLICHTING,W.KABSCH, S.SCHULTZ,A.F.V.WAGNER (1998)
BIOCHEM.BIOPHYS.RES.COMM. 246, 342, pH 7.4
|
Resolution 2.50 Å R-free 0.272 |
| 1BS7 PEPTIDE DEFORMYLASE AS NI2+ CONTAINING FORM Deposited 1998-09-01 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–168（168 aa）
|
Not recorded | NI NICKEL (II) ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 7.4；SEE: D.GROCHE,A.BECKER,I.SCHLICHTING,W.KABSCH, S.SCHULTZ,A.F.V.WAGNER (1998)
BIOCHEM.BIOPHYS.RES.COMM. 246, 342, pH 7.4
|
Resolution 2.50 Å R-free 0.272 |
| 1BS8 PEPTIDE DEFORMYLASE AS ZN2+ CONTAINING FORM IN COMPLEX WITH TRIPEPTIDE MET-ALA-SER Deposited 1998-09-01 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–168（168 aa）
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 7.4；SEE: D.GROCHE,A.BECKER,I.SCHLICHTING,W.KABSCH, S.SCHULTZ,A.F.V.WAGNER (1998)
BIOCHEM.BIOPHYS.RES.COMM. 246, 342, pH 7.4
|
Resolution 2.20 Å R-free 0.261 |
| 1BS8 PEPTIDE DEFORMYLASE AS ZN2+ CONTAINING FORM IN COMPLEX WITH TRIPEPTIDE MET-ALA-SER Deposited 1998-09-01 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–168（168 aa）
|
Not recorded | ZN ZINC ION × 1 SO4 SULFATE ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 7.4；SEE: D.GROCHE,A.BECKER,I.SCHLICHTING,W.KABSCH, S.SCHULTZ,A.F.V.WAGNER (1998)
BIOCHEM.BIOPHYS.RES.COMM. 246, 342, pH 7.4
|
Resolution 2.20 Å R-free 0.261 |
| 1BS8 PEPTIDE DEFORMYLASE AS ZN2+ CONTAINING FORM IN COMPLEX WITH TRIPEPTIDE MET-ALA-SER Deposited 1998-09-01 | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain C
1–168（168 aa）
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 7.4；SEE: D.GROCHE,A.BECKER,I.SCHLICHTING,W.KABSCH, S.SCHULTZ,A.F.V.WAGNER (1998)
BIOCHEM.BIOPHYS.RES.COMM. 246, 342, pH 7.4
|
Resolution 2.20 Å R-free 0.261 |
| 1BSJ COBALT DEFORMYLASE INHIBITOR COMPLEX FROM E.COLI Deposited 1998-08-28 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
2–169（168 aa）
|
Not recorded | CO COBALT (II) ION × 1 PO4 PHOSPHATE ION × 1 MLN (S)-2-(PHOSPHONOXY)CAPROYL-L-LEUCYL-P-NITROANILIDE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 7.5；pH 7.5
|
Resolution 3.00 Å R-free 0.207 |
| 1BSK ZINC DEFORMYLASE INHIBITOR COMPLEX FROM E.COLI Deposited 1998-08-28 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
2–169（168 aa）
|
Not recorded | ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1 MLN (S)-2-(PHOSPHONOXY)CAPROYL-L-LEUCYL-P-NITROANILIDE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 7.5；pH 7.5
|
Resolution 3.00 Å R-free 0.221 |
| 1BSZ PEPTIDE DEFORMYLASE AS FE2+ CONTAINING FORM (NATIVE) IN COMPLEX WITH INHIBITOR POLYETHYLENE GLYCOL Deposited 1998-09-01 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–168（168 aa）
|
Not recorded | FE FE (III) ION × 1 2PE NONAETHYLENE GLYCOL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 7.4；SEE: D.GROCHE,A.BECKER,I.SCHLICHTING,W.KABSCH, S.SCHULTZ,A.F.V.WAGNER (1998)
BIOCHEM.BIOPHYS.RES.COMM. 246, 342, pH 7.4
|
Resolution 1.90 Å R-free 0.247 |
| 1BSZ PEPTIDE DEFORMYLASE AS FE2+ CONTAINING FORM (NATIVE) IN COMPLEX WITH INHIBITOR POLYETHYLENE GLYCOL Deposited 1998-09-01 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–168（168 aa）
|
Not recorded | FE FE (III) ION × 1 2PE NONAETHYLENE GLYCOL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 7.4；SEE: D.GROCHE,A.BECKER,I.SCHLICHTING,W.KABSCH, S.SCHULTZ,A.F.V.WAGNER (1998)
BIOCHEM.BIOPHYS.RES.COMM. 246, 342, pH 7.4
|
Resolution 1.90 Å R-free 0.247 |
| 1BSZ PEPTIDE DEFORMYLASE AS FE2+ CONTAINING FORM (NATIVE) IN COMPLEX WITH INHIBITOR POLYETHYLENE GLYCOL Deposited 1998-09-01 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–168（168 aa）
|
Not recorded | FE FE (III) ION × 1 2PE NONAETHYLENE GLYCOL × 1 SO4 SULFATE ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 7.4；SEE: D.GROCHE,A.BECKER,I.SCHLICHTING,W.KABSCH, S.SCHULTZ,A.F.V.WAGNER (1998)
BIOCHEM.BIOPHYS.RES.COMM. 246, 342, pH 7.4
|
Resolution 1.90 Å R-free 0.247 |
| 1DEF PEPTIDE DEFORMYLASE CATALYTIC CORE (RESIDUES 1-147), NMR, 9 STRUCTURES Deposited 1996-03-19 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–147（147 aa）
Fragment：ACTIVE CATALYTIC CORE, RESIDUES 1 - 147
|
Not recorded | ZN ZINC ION × 1 | SOLUTION NMR |
NMR measurement conditions
pH 7.2；318 K
|
Resolution not provided |
| 1DFF PEPTIDE DEFORMYLASE Deposited 1997-08-19 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–164（164 aa）
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION | mmCIF provides none of the parsed conditions | Resolution 2.88 Å R-free 0.289 |
| 1G27 CRYSTAL STRUCTURE OF E.COLI POLYPEPTIDE DEFORMYLASE COMPLEXED WITH THE INHIBITOR BB-3497 Deposited 2000-10-17 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–168（168 aa）
|
Not recorded | NI NICKEL (II) ION × 1 BB1 2-[(FORMYL-HYDROXY-AMINO)-METHYL]-HEXANOIC ACID (1-DIMETHYLCARBAMOYL-2,2-DIMETHYL-PROPYL)-AMIDE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；290 K；10mg/ml PDF, 20mM BB-3497, 25% PEG 4000, 0.1M sodium citrate, 0.2M ammonium acetate,
pH 5.6, VAPOR DIFFUSION, HANGING DROP at 290K
|
Resolution 2.10 Å R-free 0.270 |
| 1G27 CRYSTAL STRUCTURE OF E.COLI POLYPEPTIDE DEFORMYLASE COMPLEXED WITH THE INHIBITOR BB-3497 Deposited 2000-10-17 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–168（168 aa）
|
Not recorded | NI NICKEL (II) ION × 1 BB1 2-[(FORMYL-HYDROXY-AMINO)-METHYL]-HEXANOIC ACID (1-DIMETHYLCARBAMOYL-2,2-DIMETHYL-PROPYL)-AMIDE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；290 K；10mg/ml PDF, 20mM BB-3497, 25% PEG 4000, 0.1M sodium citrate, 0.2M ammonium acetate,
pH 5.6, VAPOR DIFFUSION, HANGING DROP at 290K
|
Resolution 2.10 Å R-free 0.270 |
| 1G27 CRYSTAL STRUCTURE OF E.COLI POLYPEPTIDE DEFORMYLASE COMPLEXED WITH THE INHIBITOR BB-3497 Deposited 2000-10-17 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–168（168 aa）
|
Not recorded | NI NICKEL (II) ION × 1 BB1 2-[(FORMYL-HYDROXY-AMINO)-METHYL]-HEXANOIC ACID (1-DIMETHYLCARBAMOYL-2,2-DIMETHYL-PROPYL)-AMIDE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；290 K；10mg/ml PDF, 20mM BB-3497, 25% PEG 4000, 0.1M sodium citrate, 0.2M ammonium acetate,
pH 5.6, VAPOR DIFFUSION, HANGING DROP at 290K
|
Resolution 2.10 Å R-free 0.270 |
| 1G2A THE CRYSTAL STRUCTURE OF E.COLI PEPTIDE DEFORMYLASE COMPLEXED WITH ACTINONIN Deposited 2000-10-18 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–168（168 aa）
|
Not recorded | NI NICKEL (II) ION × 1 BB2 ACTINONIN × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；10mg/ml PDF, 20mM actinonin, 50mM HEPES, pH 7.5 + 25-32% PEG 4000, 0.1M sodium citrate, pH 5.6, 0.2M ammonium acetate, VAPOR DIFFUSION, HANGING DROP at 290K
|
Resolution 1.75 Å R-free 0.250 |
| 1G2A THE CRYSTAL STRUCTURE OF E.COLI PEPTIDE DEFORMYLASE COMPLEXED WITH ACTINONIN Deposited 2000-10-18 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–168（168 aa）
|
Not recorded | NI NICKEL (II) ION × 1 BB2 ACTINONIN × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；10mg/ml PDF, 20mM actinonin, 50mM HEPES, pH 7.5 + 25-32% PEG 4000, 0.1M sodium citrate, pH 5.6, 0.2M ammonium acetate, VAPOR DIFFUSION, HANGING DROP at 290K
|
Resolution 1.75 Å R-free 0.250 |
| 1G2A THE CRYSTAL STRUCTURE OF E.COLI PEPTIDE DEFORMYLASE COMPLEXED WITH ACTINONIN Deposited 2000-10-18 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–168（168 aa）
|
Not recorded | NI NICKEL (II) ION × 1 BB2 ACTINONIN × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；10mg/ml PDF, 20mM actinonin, 50mM HEPES, pH 7.5 + 25-32% PEG 4000, 0.1M sodium citrate, pH 5.6, 0.2M ammonium acetate, VAPOR DIFFUSION, HANGING DROP at 290K
|
Resolution 1.75 Å R-free 0.250 |
| 1ICJ PDF PROTEIN IS CRYSTALLIZED AS NI2+ CONTAINING FORM, COCRYSTALLIZED WITH INHIBITOR POLYETHYLENE GLYCOL (PEG) Deposited 1998-03-12 | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
1–168（168 aa）
Chain B
1–168（168 aa）
Chain C
1–168（168 aa）
|
Not recorded | NI NICKEL (II) ION × 3 2PE NONAETHYLENE GLYCOL × 3 SO4 SULFATE ION × 2 | X-RAY DIFFRACTION | mmCIF provides none of the parsed conditions | Resolution 1.90 Å R-free 0.230 |
| 1LRU Crystal Structure of E.coli Peptide Deformylase Complexed with Antibiotic Actinonin Deposited 2002-05-16 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–168（168 aa）
|
Not recorded | ZN ZINC ION × 1 BB2 ACTINONIN × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；290 K；0.5M (NH4)2SO4, 28%PEG400, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
|
Resolution 2.10 Å |
| 1LRU Crystal Structure of E.coli Peptide Deformylase Complexed with Antibiotic Actinonin Deposited 2002-05-16 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–168（168 aa）
|
Not recorded | ZN ZINC ION × 1 BB2 ACTINONIN × 1 SO4 SULFATE ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；290 K；0.5M (NH4)2SO4, 28%PEG400, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
|
Resolution 2.10 Å |
| 1LRU Crystal Structure of E.coli Peptide Deformylase Complexed with Antibiotic Actinonin Deposited 2002-05-16 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–168（168 aa）
|
Not recorded | ZN ZINC ION × 1 BB2 ACTINONIN × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；290 K；0.5M (NH4)2SO4, 28%PEG400, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
|
Resolution 2.10 Å |
| 1LRU Crystal Structure of E.coli Peptide Deformylase Complexed with Antibiotic Actinonin Deposited 2002-05-16 | Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–168（168 aa）
Chain C
1–168（168 aa）
|
Not recorded | ZN ZINC ION × 2 BB2 ACTINONIN × 2 SO4 SULFATE ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；290 K；0.5M (NH4)2SO4, 28%PEG400, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
|
Resolution 2.10 Å |
| 1XEM High Resolution Crystal Structure of Escherichia coli Zinc- Peptide Deformylase bound to formate Deposited 2004-09-10 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–168（168 aa）
|
Not recorded | ZN ZINC ION × 1 FMT FORMIC ACID × 10 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；Sodium Acetate, Sodium Formate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.76 Å R-free 0.204 |
| 1XEN High Resolution Crystal Structure of Escherichia coli Iron- Peptide Deformylase Bound To Formate Deposited 2004-09-10 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–168（168 aa）
|
Not recorded | FE FE (III) ION × 1 FMT FORMIC ACID × 6 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；Sodium Acetate, Sodium Formate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.85 Å R-free 0.218 |
| 1XEO High Resolution Crystals Structure of Cobalt- Peptide Deformylase Bound To Formate Deposited 2004-09-10 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–168（168 aa）
|
Not recorded | CO COBALT (II) ION × 1 FMT FORMIC ACID × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；Sodium Acetate, Sodium Formate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.30 Å R-free 0.215 |
| 2AI8 E.coli Polypeptide Deformylase complexed with SB-485343 Deposited 2005-07-29 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–168（168 aa）
|
Not recorded | NI NICKEL (II) ION × 1 SB7 [HYDROXY(3-PHENYLPROPYL)AMINO]METHANOL × 1 | X-RAY DIFFRACTION | mmCIF provides none of the parsed conditions | Resolution 1.70 Å R-free 0.226 |
| 2AI8 E.coli Polypeptide Deformylase complexed with SB-485343 Deposited 2005-07-29 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–168（168 aa）
|
Not recorded | NI NICKEL (II) ION × 1 SB7 [HYDROXY(3-PHENYLPROPYL)AMINO]METHANOL × 1 | X-RAY DIFFRACTION | mmCIF provides none of the parsed conditions | Resolution 1.70 Å R-free 0.226 |
| 2AI8 E.coli Polypeptide Deformylase complexed with SB-485343 Deposited 2005-07-29 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–168（168 aa）
|
Not recorded | NI NICKEL (II) ION × 1 SB7 [HYDROXY(3-PHENYLPROPYL)AMINO]METHANOL × 1 | X-RAY DIFFRACTION | mmCIF provides none of the parsed conditions | Resolution 1.70 Å R-free 0.226 |
| 2DEF PEPTIDE DEFORMYLASE CATALYTIC CORE (RESIDUES 1-147), NMR, 20 STRUCTURES Deposited 1997-12-15 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
2–147（146 aa）
Fragment：ACTIVE CATALYTIC CORE, RESIDUES 1 - 147
|
Mutation：S1A | NI NICKEL (II) ION × 1 | SOLUTION NMR |
NMR measurement conditions
pH 7.2；318 K
|
Resolution not provided |
| 2KMN Solution structure of peptide deformylase complexed with actinonin Deposited 2009-08-01 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
2–148（147 aa）
|
Not recorded | ZN ZINC ION × 1 BB2 ACTINONIN × 1 | SOLUTION NMR |
NMR measurement conditions
pH 7.2；310 K；Ionic strength (raw mmCIF value) 10；Pressure ambient
NMR sample composition
0.6-1.0 mM [U-100% 13C; U-100% 15N] Protein-1, 1.2 mM ACTINONIN-2, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 2W3T Chloro complex of the Ni-Form of E.coli deformylase Deposited 2008-11-14 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
2–169（168 aa）
Fragment：RESIDUES 2-169
|
Not recorded | NI NICKEL (II) ION × 1 CL CHLORIDE ION × 1 EOH ETHANOL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 4；293 K；20.5% PEG4000, 100MM NAOAC PH 4.0, 293 K
|
Resolution 1.69 Å R-free 0.243 |
| 2W3U formate complex of the Ni-Form of E.coli deformylase Deposited 2008-11-14 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
2–169（168 aa）
Fragment：RESIDUES 2-169
|
Not recorded | NI NICKEL (II) ION × 1 FMT FORMIC ACID × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 4.1；293 K；20% PEG4000, 0.2M (NH4)2SO4, 0.1M NAOAC PH 4.1, 293 K
|
Resolution 1.96 Å R-free 0.285 |
| 3K6L The structure of E.coli peptide deformylase (PDF) in complex with peptidomimetic ligand BB2827 Deposited 2009-10-09 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–169（169 aa）
|
Not recorded | NI NICKEL (II) ION × 1 2BB (2S,3R)-N~4~-[(1S)-1-(dimethylcarbamoyl)-2,2-dimethylpropyl]-N~1~,2-dihydroxy-3-(2-methylpropyl)butanediamide × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；20% PEG3350, 0.2M Potassium formate, VAPOR DIFFUSION, SITTING DROP, temperature 294K
|
Resolution 2.15 Å R-free 0.319 |
| 3K6L The structure of E.coli peptide deformylase (PDF) in complex with peptidomimetic ligand BB2827 Deposited 2009-10-09 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–169（169 aa）
|
Not recorded | NI NICKEL (II) ION × 1 2BB (2S,3R)-N~4~-[(1S)-1-(dimethylcarbamoyl)-2,2-dimethylpropyl]-N~1~,2-dihydroxy-3-(2-methylpropyl)butanediamide × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；20% PEG3350, 0.2M Potassium formate, VAPOR DIFFUSION, SITTING DROP, temperature 294K
|
Resolution 2.15 Å R-free 0.319 |
| 3K6L The structure of E.coli peptide deformylase (PDF) in complex with peptidomimetic ligand BB2827 Deposited 2009-10-09 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–169（169 aa）
|
Not recorded | NI NICKEL (II) ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；20% PEG3350, 0.2M Potassium formate, VAPOR DIFFUSION, SITTING DROP, temperature 294K
|
Resolution 2.15 Å R-free 0.319 |
| 4AL2 peptide deformylase (Ni-form) with hydrosulfide Deposited 2012-02-29 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
2–169（168 aa）
|
Not recorded | NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 4.6；293 K；25% PEG 4000, 200 MM NAOAC PH 4.6, 293 K, INCUBATED IN H2S ATMOSPHERE EQUILIBRATED WITH 50 MM NA2S AT PH 4.6
|
Resolution 2.60 Å R-free 0.298 |
| 4AL2 peptide deformylase (Ni-form) with hydrosulfide Deposited 2012-02-29 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
2–169（168 aa）
|
Not recorded | NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 4.6；293 K；25% PEG 4000, 200 MM NAOAC PH 4.6, 293 K, INCUBATED IN H2S ATMOSPHERE EQUILIBRATED WITH 50 MM NA2S AT PH 4.6
|
Resolution 2.60 Å R-free 0.298 |
| 4AL2 peptide deformylase (Ni-form) with hydrosulfide Deposited 2012-02-29 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
2–169（168 aa）
|
Not recorded | NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 4.6；293 K；25% PEG 4000, 200 MM NAOAC PH 4.6, 293 K, INCUBATED IN H2S ATMOSPHERE EQUILIBRATED WITH 50 MM NA2S AT PH 4.6
|
Resolution 2.60 Å R-free 0.298 |
| 4AL3 peptide deformylase (Co-form) with mercaptoethanol Deposited 2012-02-29 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
2–169（168 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | CO COBALT (II) ION × 1 CL CHLORIDE ION × 1 BME BETA-MERCAPTOETHANOL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 6；293 K；20.5% PEG 4000, 100 MM NA-ACETATE PH 4.0, 293 K. TRANSFERRED TO 20% PEG, 50 MM ACETATE PH 6.0, THEN SOAKED WITH 10 MM MERCAPTOETHANOL
|
Resolution 1.98 Å R-free 0.276 |
| 4AZ4 E.coli deformylase with Co(II) and hydrosulfide Deposited 2012-06-22 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
2–169（168 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | CO COBALT (II) ION × 1 H2S HYDROSULFURIC ACID × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 4.6；293 K；2 UL PROTEIN PLUS 2 UL (20% PEG 4000, 0.1 M NAOAC PH 4.6), 293 K. SOAKED IN 10% PEG4000, 20% PEG400, 0.1 M NAOAC PH 4.6, 293 K, FOR 1 DAY. INCUBATED IN H2S ATMOSPHERE EQUILIBRATED WITH 50 MM NA2S AT PH 4.6
|
Resolution 1.80 Å R-free 0.221 |
| 4V5B Structure of PDF binding helix in complex with the ribosome. Deposited 2007-11-22 | Assembly 1 Insufficient information Heteromer；Protein × 50 PDB declaration: 53-meric（53） Consistent with all polymers |
Chain A5
147–162（16 aa）
|
Mutation：YES | MG MAGNESIUM ION × 170 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 7.5；pH 7.5
|
Resolution 3.74 Å R-free 0.323 |
| 6IY7 E. coli peptide deformylase crystal structure fitted into the cryo-EM density map of E. coli 70S ribosome in complex with peptide deformylase Deposited 2018-12-13 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain P
1–169（169 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 10.50 Å |
| 6IZI Crystal structure of E. coli peptide deformylase and methionine aminopeptidase fitted into the cryo-EM density map of the complex Deposited 2018-12-19 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain P
1–169（169 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 11.80 Å |
| 7D6Z Molecular model of the cryo-EM structure of 70S ribosome in complex with peptide deformylase and trigger factor Deposited 2020-10-02 | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 58-meric（58） Consistent with all polymers |
Chain g
1–169（169 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7D80 Molecular model of the cryo-EM structure of 70S ribosome in complex with peptide deformylase, trigger factor, and methionine aminopeptidase Deposited 2020-10-06 | Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 57-meric（57） Consistent with all polymers |
Chain 3
1–169（169 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |