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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Enzyme Classification Number = 3.5.1.88

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Search Summary

This query matches 174 Structures.

Refinements

Structure Determination Methodology

experimental (174)

Scientific Name of Source Organism

	Escherichia coli (21)
	Arabidopsis thaliana (18)
	Xanthomonas oryzae pv. oryzae KACC 10331 (17)
	Pseudomonas aeruginosa (12)
	Streptococcus agalactiae (12)
	Escherichia coli K-12 (10)
	Staphylococcus aureus (10)
	Streptococcus pneumoniae (9)
	Acinetobacter baumannii (7)
	Acinetobacter baumannii MRSN 3527 (6)

More...

Taxonomy

	Bacteria (152)
	Eukaryota (23)
	other sequences (3)

Experimental Method

	X-RAY DIFFRACTION (166)
	ELECTRON MICROSCOPY (5)
	SOLUTION NMR (3)

Polymer Entity Type

	Protein (174)
	RNA (3)

Refinement Resolution (Å)

	1.0 - 1.5 (7)
	1.5 - 2.0 (65)
	2.0 - 2.5 (67)
	2.5 - 3.0 (19)
	3.0 - 3.5 (8)
	3.5 - 4.0 (1)
	4.0 - 4.5 (1)
	> 4.5 (3)

Release Date

	1995 - 1999 (10)
	2000 - 2004 (21)
	2005 - 2009 (36)
	2010 - 2014 (34)
	2015 - 2019 (43)
	2020 - 2024 (30)

Enzyme Classification Name

	Hydrolases (174)
	Isomerases (3)

Symmetry Type

	Asymmetric (134)
	Cyclic (47)
	Dihedral (2)

SCOP Classification

	Alpha and beta proteins (a+b) (144)
	Artifacts (28)

AllSelected

1 to 25 of 174 Structures

Page 1 of 7

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1BS4 \| pdb_00001bs4	Download File View File

PEPTIDE DEFORMYLASE AS ZN2+ CONTAINING FORM (NATIVE) IN COMPLEX WITH INHIBITOR POLYETHYLENE GLYCOL

Becker, A., Schlichting, I., Kabsch, W., Groche, D., Schultz, S., Wagner, A.F.V.

(1998) Nat Struct Biol 5: 1053-1058

Released	1999-08-27
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Escherichia coli
Macromolecule	PROTEIN (PEPTIDE DEFORMYLASE) (protein)
Unique Ligands	2PE, SO4, ZN

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1BS5 \| pdb_00001bs5	Download File View File

PEPTIDE DEFORMYLASE AS ZN2+ CONTAINING FORM

Becker, A., Schlichting, I., Kabsch, W., Groche, D., Schultz, S., Wagner, A.F.V.

(1998) Nat Struct Biol 5: 1053-1058

Released	1999-08-27
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Escherichia coli
Macromolecule	PROTEIN (PEPTIDE DEFORMYLASE) (protein)
Unique Ligands	SO4, ZN

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1BS6 \| pdb_00001bs6	Download File View File

PEPTIDE DEFORMYLASE AS NI2+ CONTAINING FORM IN COMPLEX WITH TRIPEPTIDE MET-ALA-SER

Becker, A., Schlichting, I., Kabsch, W., Groche, D., Schultz, S., Wagner, A.F.V.

(1998) Nat Struct Biol 5: 1053-1058

Released	1999-08-27
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Escherichia coli
Macromolecule	PROTEIN (MET-ALA-SER) (protein) PROTEIN (PEPTIDE DEFORMYLASE) (protein)
Unique Ligands	NI, SO4

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1BS7 \| pdb_00001bs7	Download File View File

PEPTIDE DEFORMYLASE AS NI2+ CONTAINING FORM

Becker, A., Schlichting, I., Kabsch, W., Groche, D., Schultz, S., Wagner, A.F.V.

(1998) J Biological Chem 273: 11413-11416

Released	1999-08-27
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Escherichia coli
Macromolecule	PROTEIN (PEPTIDE DEFORMYLASE) (protein)
Unique Ligands	NI, SO4

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1BS8 \| pdb_00001bs8	Download File View File

PEPTIDE DEFORMYLASE AS ZN2+ CONTAINING FORM IN COMPLEX WITH TRIPEPTIDE MET-ALA-SER

Becker, A., Schlichting, I., Kabsch, W., Groche, D., Schultz, S., Wagner, A.F.V.

(1998) Nat Struct Biol 5: 1053-1058

Released	1999-08-27
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Escherichia coli
Macromolecule	PROTEIN (MET-ALA-SER) (protein) PROTEIN (PEPTIDE DEFORMYLASE) (protein)
Unique Ligands	SO4, ZN

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1BSJ \| pdb_00001bsj	Download File View File

COBALT DEFORMYLASE INHIBITOR COMPLEX FROM E.COLI

Hao, B., Gong, W., Rajagopalan, P.T., Hu, Y., Pei, D., Chan, M.K.

(1999) Biochemistry 38: 4712-4719

Released	2000-04-15
Method	X-RAY DIFFRACTION 3 Å
Organisms	Escherichia coli
Macromolecule	PROTEIN (PEPTIDE DEFORMYLASE) (protein)
Unique Ligands	CO, MLN, PO4

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1BSK \| pdb_00001bsk	Download File View File

ZINC DEFORMYLASE INHIBITOR COMPLEX FROM E.COLI

Hao, B., Gong, W., Rajagopalan, P.T., Hu, Y., Pei, D., Chan, M.K.

(1999) Biochemistry 38: 4712-4719

Released	2000-04-15
Method	X-RAY DIFFRACTION 3 Å
Organisms	Escherichia coli
Macromolecule	PROTEIN (PEPTIDE DEFORMYLASE) (protein)
Unique Ligands	MLN, PO4, ZN

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1BSZ \| pdb_00001bsz	Download File View File

PEPTIDE DEFORMYLASE AS FE2+ CONTAINING FORM (NATIVE) IN COMPLEX WITH INHIBITOR POLYETHYLENE GLYCOL

Becker, A., Schlichting, I., Kabsch, W., Groche, D., Schultz, S., Wagner, A.F.V.

(1998) Nat Struct Biol 5: 1053-1058

Released	1999-08-26
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Escherichia coli K-12
Macromolecule	PROTEIN (PEPTIDE DEFORMYLASE) (protein)
Unique Ligands	2PE, FE, SO4

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1DEF \| pdb_00001def	Download File View File

PEPTIDE DEFORMYLASE CATALYTIC CORE (RESIDUES 1-147), NMR, 9 STRUCTURES

Meinnel, T., Dardel, F.

(1996) J Mol Biology 262: 375-386

Released	1997-04-21
Method	SOLUTION NMR
Organisms	Escherichia coli
Macromolecule	PEPTIDE DEFORMYLASE (protein)
Unique Ligands	ZN

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1DFF \| pdb_00001dff	Download File View File

PEPTIDE DEFORMYLASE

Chan, M.K., Gong, W., Rajagopalan, P.T.R., Hao, B., Tsai, C.M., Pei, D.

(1997) Biochemistry 36: 13904-13909

Released	1998-09-02
Method	X-RAY DIFFRACTION 2.88 Å
Organisms	Escherichia coli
Macromolecule	PEPTIDE DEFORMYLASE (protein)
Unique Ligands	ZN

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1G27 \| pdb_00001g27	Download File View File

CRYSTAL STRUCTURE OF E.COLI POLYPEPTIDE DEFORMYLASE COMPLEXED WITH THE INHIBITOR BB-3497

Clements, J.M., Beckett, P., Brown, A., Catlin, C., Lobell, M., Palan, S., Thomas, W., Whittaker, M., Baker, P.J., Rodgers, H.F., Barynin, V., Rice, D.W., Hunter, M.G.

(2001) Antimicrob Agents Chemother 45: 563-570

Released	2001-10-17
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Escherichia coli
Macromolecule	POLYPEPTIDE DEFORMYLASE (protein)
Unique Ligands	BB1, NI

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1G2A \| pdb_00001g2a	Download File View File

THE CRYSTAL STRUCTURE OF E.COLI PEPTIDE DEFORMYLASE COMPLEXED WITH ACTINONIN

Clements, J.M., Beckett, P., Brown, A., Catlin, C., Lobell, M., Palan, S., Thomas, W., Whittaker, M., Baker, P.J., Rodgers, H.F., Barynin, V., Rice, D.W., Hunter, M.G.

(2001) Antimicrob Agents Chemother 45: 563-570

Released	2001-10-17
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Escherichia coli
Macromolecule	POLYPEPTIDE DEFORMYLASE (protein)
Unique Ligands	BB2, NI

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1ICJ \| pdb_00001icj	Download File View File

PDF PROTEIN IS CRYSTALLIZED AS NI2+ CONTAINING FORM, COCRYSTALLIZED WITH INHIBITOR POLYETHYLENE GLYCOL (PEG)

Becker, A., Schlichting, I., Kabsch, W., Schultz, S., Wagner, A.F.V.

(1998) J Biological Chem 273: 11413-11416

Released	1999-03-23
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Escherichia coli K-12
Macromolecule	PEPTIDE DEFORMYLASE (protein)
Unique Ligands	2PE, NI, SO4

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1IX1 \| pdb_00001ix1	Download File View File

Crystal Structure of P.aeruginosa Peptide deformylase Complexed with Antibiotic Actinonin

Kim, H.-W., Yoon, H.-J., Lee, J.Y., Han, B.W., Yang, J.K., Lee, B.I., Ahn, H.J., Lee, H.H., Suh, S.W.

(2004) Proteins 57: 639-642

Released	2003-09-09
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Pseudomonas aeruginosa
Macromolecule	peptide deformylase (protein)
Unique Ligands	BB2, MHA, ZN

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1JYM \| pdb_00001jym	Download File View File

Crystals of Peptide Deformylase from Plasmodium falciparum with Ten Subunits per Asymmetric Unit Reveal Critical Characteristics of the Active Site for Drug Design

Kumar, A., Nguyen, K.T., Srivathsan, S., Ornstein, B., Turley, S., Hirsh, I., Pei, D., Hol, W.G.J.

(2002) Structure 10: 357-367

Released	2002-03-13
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Plasmodium falciparum
Macromolecule	Peptide Deformylase (protein)
Unique Ligands	CO

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1LM4 \| pdb_00001lm4	Download File View File

Structure of Peptide Deformylase from Staphylococcus aureus at 1.45 A

Kreusch, A., Spraggon, G., Lee, C.C., Klock, H., McMullan, D., Ng, K., Shin, T., Vincent, J., Warner, I., Ericson, C., Lesley, S.A.

(2003) J Mol Biology 330: 309-321

Released	2003-06-24
Method	X-RAY DIFFRACTION 1.45 Å
Organisms	Staphylococcus aureus
Macromolecule	peptide deformylase PDF1 (protein)
Unique Ligands	FE, GOL

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1LM6 \| pdb_00001lm6	Download File View File

Crystal Structure of Peptide Deformylase from Streptococcus pneumoniae

Kreusch, A., Spraggon, G., Lee, C.C., Klock, H., McMullan, D., Ng, K., Shin, T., Vincent, J., Warner, I., Ericson, C., Lesley, S.A.

(2003) J Mol Biology 330: 309-321

Released	2003-06-24
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Streptococcus pneumoniae
Macromolecule	peptide deformylase DEFB (protein)
Unique Ligands	FE, GOL

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1LME \| pdb_00001lme	Download File View File

Crystal Structure of Peptide Deformylase from Thermotoga maritima

Kreusch, A., Spraggon, G., Lee, C.C., Klock, H., McMullan, D., Ng, K., Shin, T., Vincent, J., Warner, I., Ericson, C., Lesley, S.A., Joint Center for Structural Genomics (JCSG)

(2003) J Mol Biology 330: 309-321

Released	2003-06-24
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Thermotoga maritima
Macromolecule	peptide deformylase (protein)

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1LMH \| pdb_00001lmh	Download File View File

Crystal Structure of S. aureus peptide deformylase

Baldwin, E.T., Harris, M.S.

(2002) J Biological Chem 277: 31163-31171

Released	2002-06-12
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Staphylococcus aureus
Macromolecule	PROTEIN (S.aureus peptide deformylase) (protein)
Unique Ligands	ZN

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1LQW \| pdb_00001lqw	Download File View File

Crystal Structure of S.aureus Peptide Deformylase

Mikol, V.

(2002) J Mol Biology 320: 951-962

Released	2002-07-24
Method	X-RAY DIFFRACTION 1.87 Å
Organisms	Staphylococcus aureus
Macromolecule	PEPTIDE DEFORMYLASE PDF1 (protein)
Unique Ligands	ZN

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1LQY \| pdb_00001lqy	Download File View File

Crystal Structure of Bacillus stearothermophilus Peptide Deformylase Complexed with Antibiotic Actinonin

Mathieu, M., Mikol, V.

(2002) J Mol Biology 320: 951-962

Released	2002-07-24
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Geobacillus stearothermophilus
Macromolecule	PEPTIDE deformylase 2 (protein)
Unique Ligands	BB2, NI