2gu4

E. coli methionine aminopeptidase in complex with NleP, 1: 0.5, di-metalated

Method: X-RAY DIFFRACTION D_max: 86.7 Å Quality: GOOD

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Methionine aminopeptidase

Escherichia coli

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 2–264	Not recorded	MN MANGANESE (II) ION × 2 NA SODIUM ION × 1 NLP (1-AMINO-PENTYL)-PHOSPHONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；15% PEG 20000, 0.1 M MES (pH 6.5) , VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.80 Å R-free 0.227
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 2–264	Not recorded	MN MANGANESE (II) ION × 2 NA SODIUM ION × 1 NLP (1-AMINO-PENTYL)-PHOSPHONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；15% PEG 20000, 0.1 M MES (pH 6.5) , VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.80 Å R-free 0.227

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 2GU4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2EVC Crystal structure of E. Coli. methionine amino peptidase in complex with 5-(2-(trifluoromethyl)phenyl)furan-2-carboxylic acid Deposited 2005-10-31	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–264（264 aa）	Not recorded	MN MANGANESE (II) ION × 2 NA SODIUM ION × 1 FC3 5-[2-(TRIFLUOROMETHYL)PHENYL]-2-FUROIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；292 K；15% PEG 8000, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, temperature 292K	Resolution 1.60 Å R-free 0.229
2EVM crystal structure of methionine aminopeptidase in complex with 5-(2,5-dichlorophenyl)furan-2-carboxylic acid Deposited 2005-10-31	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–264（264 aa）	Not recorded	MN MANGANESE (II) ION × 2 NA SODIUM ION × 1 FC2 5-(2,5-DICHLOROPHENYL)-2-FUROIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；292 K；15% PEG 8000, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, temperature 292K	Resolution 1.70 Å R-free 0.248
2EVO crystal structure of methionine amino peptidase in complex with N-cyclopentyl-N-(thiazol-2-yl)oxalamide Deposited 2005-10-31	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–264（264 aa）	Not recorded	CO COBALT (II) ION × 3 CT0 N1-CYCLOPENTYL-N2-(THIAZOL-2-YL)OXALAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；292 K；15% PEG 8000, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, temperature 292K	Resolution 1.70 Å R-free 0.241
2EVO crystal structure of methionine amino peptidase in complex with N-cyclopentyl-N-(thiazol-2-yl)oxalamide Deposited 2005-10-31	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–264（264 aa）	Not recorded	CO COBALT (II) ION × 3 CT0 N1-CYCLOPENTYL-N2-(THIAZOL-2-YL)OXALAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；292 K；15% PEG 8000, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, temperature 292K	Resolution 1.70 Å R-free 0.241
2GG0 Novel bacterial methionine aminopeptidase inhibitors Deposited 2006-03-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–264（263 aa）	Not recorded	CO COBALT (II) ION × 2 NA SODIUM ION × 1 U11 METHYL N-{(2S,3R)-3-AMINO-2-HYDROXY-3-[4-(TRIFLUOROMETHYL)PHENYL]PROPANOYL}ALANYLGLYCINATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions batch；pH 7；298 K；10 mg/ml protein, 25% PEG 8000, 100 mM TRIS-HCl, 1-5 mM inhibitor, pH 7.0, batch, temperature 298K	Resolution 1.28 Å R-free 0.209
2GG2 Novel bacterial methionine aminopeptidase inhibitors Deposited 2006-03-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–264（263 aa）	Not recorded	CO COBALT (II) ION × 2 NA SODIUM ION × 1 U12 5-IMINO-4-(3-TRIFLUOROMETHYL-PHENYLAZO)-5H-PYRAZOL-3-YLAMINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions batch；pH 7；298 K；10 mg/ml protein, 25% PEG 8000, 100 mM TRIS-HCl, 1-5 mM inhibitor, pH 7.0, batch, temperature 298K	Resolution 1.00 Å R-free 0.153
2GG3 Novel bacterial methionine aminopeptidase inhibitors Deposited 2006-03-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–264（263 aa）	Not recorded	CO COBALT (II) ION × 2 NA SODIUM ION × 1 U13 4-(4-FLUORO-PHENYLAZO)-5-IMINO-5H-PYRAZOL-3-YLAMINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；298 K；10 mg/ml protein, 25% PEG 8000, 100 mM TRIS-HCl, batch, pH 7.0, temperature 298K	Resolution 1.45 Å R-free 0.161
2GG5 Novel bacterial methionine aminopeptidase inhibitors Deposited 2006-03-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–264（263 aa）	Not recorded	CO COBALT (II) ION × 2 NA SODIUM ION × 1 U19 5-IMINO-4-(2-TRIFLUOROMETHYL-PHENYLAZO)-5H-PYRAZOL-3-YLAMINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；298 K；10 mg/ml protein, 25% PEG 8000, 100 mM TRIS-HCl, 1-5 mM inhibitor, batch, pH 7.0, temperature 298K	Resolution 2.12 Å R-free 0.300
2GG7 Novel bacterial methionine aminopeptidase inhibitors Deposited 2006-03-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–264（263 aa）	Not recorded	CO COBALT (II) ION × 2 NA SODIUM ION × 1 U14 3-(5-AMINO-3-IMINO-3H-PYRAZOL-4-YLAZO)-BENZOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions batch；pH 7；298 K；10 mg/ml protein, 25% PEG 8000, 100 mM TRIS-HCl, 1-5 mM inhibitor, pH 7.0, batch, temperature 298K	Resolution 1.12 Å R-free 0.155
2GG8 Novel bacterial methionine aminopeptidase inhibitors Deposited 2006-03-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–264（263 aa）	Not recorded	CO COBALT (II) ION × 2 NA SODIUM ION × 1 U15 METHYL N-[(2S,3R)-3-AMINO-2-HYDROXY-3-(4-METHYLPHENYL)PROPANOYL]-D-ALANYL-D-LEUCINATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions batch；pH 7；298 K；10 mg/ml protein, 25% PEG 8000, 100 mM TRIS-HCl, 1-5 mM inhibitor, pH 7.0, batch, temperature 298K	Resolution 1.80 Å R-free 0.243
2GG9 Novel bacterial methionine aminopeptidase inhibitors Deposited 2006-03-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–264（263 aa）	Not recorded	CO COBALT (II) ION × 2 NA SODIUM ION × 1 U16 METHYL N-[(2S,3R)-3-AMINO-2-HYDROXY-3-(4-ISOPROPYLPHENYL)PROPANOYL]-D-ALANYL-D-LEUCINATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions batch；pH 7；298 K；10 mg/ml protein, 25% PEG 8000, 100 mM TRIS-HCl, 1-5 mM inhibitor, pH 7.0, batch, temperature 298K	Resolution 1.05 Å R-free 0.159
2GGB Novel bacterial methionine aminopeptidase inhibitors Deposited 2006-03-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–264（263 aa）	Not recorded	CO COBALT (II) ION × 2 NA SODIUM ION × 1 U17 METHYL N-[(2S,3R)-3-AMINO-2-HYDROXYHEPTANOYL]-L-SERYL-L-LEUCINATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；298 K；10 mg/ml protein, 25% PEG 8000, 100 mM TRIS-HCl, 1-5 mM inhibitor, batch, pH 7.0, temperature 298K	Resolution 2.13 Å R-free 0.259
2GGC Novel bacterial methionine aminopeptidase inhibitors Deposited 2006-03-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–264（263 aa）	Not recorded	CO COBALT (II) ION × 2 NA SODIUM ION × 1 MET METHIONINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions batch；pH 7；298 K；10 mg/ml protein, 25% PEG 8000, 100 mM TRIS-HCl, 1-5 mM inhibitor, pH 7.0, batch, temperature 298K	Resolution 1.00 Å R-free 0.133
2GTX Structural Basis of Catalysis by Mononuclear Methionine Aminopeptidase Deposited 2006-04-28	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 4–264（261 aa）	Not recorded	MN MANGANESE (II) ION × 1 NA SODIUM ION × 1 NLP (1-AMINO-PENTYL)-PHOSPHONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；15% PEG 20000, 0.1 M MES (pH 6.5) , VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.00 Å R-free 0.241
2GTX Structural Basis of Catalysis by Mononuclear Methionine Aminopeptidase Deposited 2006-04-28	Different construct Different ligand/ion Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 4–264（261 aa）	Not recorded	MN MANGANESE (II) ION × 1 NA SODIUM ION × 1 NLP (1-AMINO-PENTYL)-PHOSPHONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；15% PEG 20000, 0.1 M MES (pH 6.5) , VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.00 Å R-free 0.241
2GU5 E. coli methionine aminopeptidase in complex with NleP, 1: 1, di-metalated Deposited 2006-04-28	Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–264（263 aa）	Not recorded	MN MANGANESE (II) ION × 2 NA SODIUM ION × 1 NLP (1-AMINO-PENTYL)-PHOSPHONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；15% PEG 20000, 0.1 M MES (pH 6.5) , VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.60 Å R-free 0.233
2GU5 E. coli methionine aminopeptidase in complex with NleP, 1: 1, di-metalated Deposited 2006-04-28	Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–264（263 aa）	Not recorded	MN MANGANESE (II) ION × 2 NA SODIUM ION × 1 NLP (1-AMINO-PENTYL)-PHOSPHONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；15% PEG 20000, 0.1 M MES (pH 6.5) , VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.60 Å R-free 0.233
2GU6 E. coli methionine aminopeptidase in complex with NleP, 1: 2, di-metalated Deposited 2006-04-28	Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–264（263 aa）	Not recorded	MN MANGANESE (II) ION × 2 NA SODIUM ION × 1 NLP (1-AMINO-PENTYL)-PHOSPHONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；15% PEG 20000, 0.1 M MES (pH 6.5) , VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.70 Å R-free 0.224
2GU6 E. coli methionine aminopeptidase in complex with NleP, 1: 2, di-metalated Deposited 2006-04-28	Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–264（263 aa）	Not recorded	MN MANGANESE (II) ION × 2 NA SODIUM ION × 1 NLP (1-AMINO-PENTYL)-PHOSPHONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；15% PEG 20000, 0.1 M MES (pH 6.5) , VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.70 Å R-free 0.224
2GU7 E. coli methionine aminopeptidase unliganded, 1:0.5 Deposited 2006-04-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–264（263 aa）	Not recorded	MN MANGANESE (II) ION × 2 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；15% PEG 20000, 0.1 M MES (pH 6.5), VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.00 Å R-free 0.244
2GU7 E. coli methionine aminopeptidase unliganded, 1:0.5 Deposited 2006-04-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–264（263 aa）	Not recorded	MN MANGANESE (II) ION × 2 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；15% PEG 20000, 0.1 M MES (pH 6.5), VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.00 Å R-free 0.244
2P98 E. coli methionine aminopeptidase monometalated with inhibitor YE7 Deposited 2007-03-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–263（262 aa）	Not recorded	MN MANGANESE (II) ION × 1 NA SODIUM ION × 1 YE7 IMIDAZO[2,1-A]ISOQUINOLINE-2-CARBOHYDRAZIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；15% PEG 20000, 0.1 M MES (pH 6.5), vapor diffusion, hanging drop, temperature 291K	Resolution 1.70 Å R-free 0.238
2P99 E. coli methionine aminopeptidase monometalated with inhibitor YE6 Deposited 2007-03-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–262（261 aa）	Not recorded	MN MANGANESE (II) ION × 1 NA SODIUM ION × 1 YE6 5-(2-chlorophenyl)furan-2-carbohydrazide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；15% PEG 20000, 0.1 M MES (pH 6.5), vapor diffusion, hanging drop, temperature 291K	Resolution 1.80 Å R-free 0.263
2P9A E. coli methionine aminopeptidase dimetalated with inhibitor YE6 Deposited 2007-03-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–263（262 aa）	Not recorded	MN MANGANESE (II) ION × 2 NA SODIUM ION × 1 YE6 5-(2-chlorophenyl)furan-2-carbohydrazide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；15% PEG 20000, 0.1 M MES (pH 6.5), vapor diffusion, hanging drop, temperature 291K	Resolution 1.60 Å R-free 0.231
2Q92 E. coli methionine aminopeptidase Mn-form with inhibitor B23 Deposited 2007-06-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–263（262 aa）	Not recorded	MN MANGANESE (II) ION × 2 NA SODIUM ION × 1 B23 5-(2-NITROPHENYL)-2-FUROIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；10-15% PEG 20000, 0.1 M MES (pH 6.5), vapor diffusion, hanging drop, temperature 291K	Resolution 1.90 Å R-free 0.238
2Q93 E. coli methionine aminopeptidase Mn-form with inhibitor B21 Deposited 2007-06-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–264（263 aa）	Not recorded	MN MANGANESE (II) ION × 2 NA SODIUM ION × 1 B21 5-(2-METHOXYPHENYL)-2-FUROIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；10-15% PEG 20000, 0.1 M MES (pH 6.5), vapor diffusion, hanging drop, temperature 291K	Resolution 1.60 Å R-free 0.251
2Q94 E. coli methionine aminopeptidase Mn-form with inhibitor A04 Deposited 2007-06-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–263（262 aa）	Not recorded	MN MANGANESE (II) ION × 2 NA SODIUM ION × 1 A04 5-[2-(TRIFLUOROMETHOXY)PHENYL]-2-FUROIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；10-15% PEG 20000, 0.1 M MES (pH 6.5), vapor diffusion, hanging drop, temperature 291K	Resolution 1.63 Å R-free 0.238
2Q95 E. coli methionine aminopeptidase Mn-form with inhibitor A05 Deposited 2007-06-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–264（263 aa）	Not recorded	MN MANGANESE (II) ION × 2 NA SODIUM ION × 1 A05 5-(2-CHLORO-4-NITROPHENYL)-2-FUROIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；10-15% PEG 20000, 0.1 M MES (pH 6.5), vapor diffusion, hanging drop, temperature 291K	Resolution 1.70 Å R-free 0.239
2Q96 E. coli methionine aminopeptidase Mn-form with inhibitor A18 Deposited 2007-06-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–264（263 aa）	Not recorded	MN MANGANESE (II) ION × 2 NA SODIUM ION × 1 A18 5-(2-CHLOROBENZYL)-2-FUROIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；10-15% PEG 20000, 0.1 M MES (pH 6.5), vapor diffusion, hanging drop, temperature 291K	Resolution 1.60 Å R-free 0.235
3D27 E. coli methionine aminopeptidase with Fe inhibitor W29 Deposited 2008-05-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 4–264（261 aa）	Not recorded	MN MANGANESE (II) ION × 2 W29 4-(3-ethylthiophen-2-yl)benzene-1,2-diol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；100 mM MES (pH 6.5), 2 mM MnCl2, 17% PEG 20000, vapor diffusion, hanging drop, temperature 298K	Resolution 2.20 Å R-free 0.244
6IZ7 E. coli methionine aminopeptidase crystal structure fitted into the cryo-EM density map of E. coli 70S ribosome in complex with methionine aminopeptidase Deposited 2018-12-18	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain P 1–264（264 aa）	Mutation：R175Q	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 11.80 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	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain Q 1–264（264 aa）	Mutation：R175Q	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 11.80 Å
6J0A Crystal structure of E. coli methionine aminopeptidase enzyme and chaperone trigger factor fitted into the cryo-EM density map of the complex Deposited 2018-12-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 1–264（264 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 14.20 Å

28 other PDB entries and 33 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	AMPM_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–263； UniProt 2–264 Author chain B； PDBConstruct 1–263； UniProt 2–264

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	2gu4
Deposition date deposition_date	2006-04-28
Structure title title	E. coli methionine aminopeptidase in complex with NleP, 1: 0.5, di-metalated
Keywords keywords	Mono-metalated, mononuclear, Mn(II)-form, hydrolase, enzyme-inhibitor complex, metalloenzyme; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	26.49 Å
Radius of gyration Rg (electron density) rg_electron	25.84 Å
Forward intensity I(0) i0	57624500.00
Molecular weight molecular_weight	58615.0 kDa
Excluded volume excluded_volume	73171 Å³
Envelope volume envelope_volume	86047 Å³
Hydration-shell volume shell_volume	27849 Å³
Envelope diameter envelope_diameter	96.3 Å
Shell Rg shell_rg	32.95 Å
Envelope Rg envelope_rg	25.83 Å
Shape Rg shape_rg	25.85 Å
Total Rg total_rg	26.56 Å
Total atoms total_atoms	4088
Residues n_residues	522
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	86.7 Å
Rg (real space) rg_real	26.52 Å
Rg uncertainty (real space) rg_real_error	0.66 Å
I(0) (real space) i0_real	5.7620e+07
I(0) uncertainty (real space) i0_real_error	9.7450e+05
Rg (reciprocal space) rg_reciprocal	26.52 Å
I(0) (reciprocal space) i0_reciprocal	57620000.0000
Solution quality estimate total_estimate	0.8103
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	85.3 Å
Skewness Skewness skewness	0.344
Kurtosis Kurtosis kurtosis	-0.474
Angular range angular_range	— – 0.3000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	19240000.0000
Real-space data points n_real_points	61
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.862; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.945; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Methionine aminopeptidase
Molecular weight formula_weight	29213.6 kDa
EC 编号 ec_number	3.4.11.18
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4409

ASSIKTPEDIEKMRVAGRLAAEVLEMIEPYVKPGVSTGELDRICNDYIVNEQHAVSACLGYHGYPKSVCISINEVVCHGIPDDAKLLKDGDIVNIDVTVIKDGFHGDTSKMFIVGKPTIMGERLCRITQESLYLALRMVKPGINLREIGAAIQKFVEAEGFSVVREYCGHGIGRGFHEEPQVLHYDSRETNVVLKPGMTFTIEPMVNAGKKEIRTMKDGWTVKTKDRSLSAQYEHTIVVTDNGCEILTLRKDDTIPAIISHDE

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	(1-AMINO-PENTYL)-PHOSPHONIC ACID
Molecular weight formula_weight	167.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	321

▼

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2gu4a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.127 — Creatinase/aminopeptidase
Superfamily Superfamily superfamily	d.127.1 — Creatinase/aminopeptidase
Family Family family	d.127.1.1 — Creatinase/aminopeptidase

Domain ID domain_id	d2gu4b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.127 — Creatinase/aminopeptidase
Superfamily Superfamily superfamily	d.127.1 — Creatinase/aminopeptidase
Family Family family	d.127.1.1 — Creatinase/aminopeptidase

CATH v4.4 (2 domains)

Domain ID domain_id	2gu4A00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	230 — Creatine Amidinohydrolase
Homologous superfamily homologous superfamily	10 — Creatinase/methionine aminopeptidase superfamily

Domain ID domain_id	2gu4B00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	230 — Creatine Amidinohydrolase
Homologous superfamily homologous superfamily	10 — Creatinase/methionine aminopeptidase superfamily

▶

8. Citations (1)

▶

Unit-cell length a length_a	49.704 Å
Unit-cell length b length_b	64.034 Å
Unit-cell length c length_c	76.347 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	108.10 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	14.853 Å
R factor r_factor	0.2060
R_work r_work	0.1950
R_free r_free	0.2270

fit	/app/data/saxs_computation/gu/2gu4/2gu4.fit
pddf	/app/data/pr_computation/gu/2gu4/2gu4.pr.out
profile	/app/data/saxs_computation/gu/2gu4/2gu4.dat