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1yvm

E. coli Methionine Aminopeptidase in complex with thiabendazole

Method: X-RAY DIFFRACTION Dmax: 57.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Methionine aminopeptidase

Escherichia coli

UniProt P07906

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 1–264 Mutation：R175Q CO COBALT (II) ION × 4 NA SODIUM ION × 1 TMG 2-(1,3-THIAZOL-4-YL)-1H-BENZIMIDAZOLE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.1；293 K；PEG 4000, cobalt chloride, hepes, methionine, sodium chloride, potassium chloride, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 1.60 Å R-free 0.233

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 1YVM Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1C21 E. COLI METHIONINE AMINOPEPTIDASE: METHIONINE COMPLEX Deposited 1999-07-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–264（263 aa） Fragment：METHIONINE
Mutation：R175Q CO COBALT (II) ION × 2 NA SODIUM ION × 1 MET METHIONINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；K2SO4, NaCl, methionine, N-octanoyl sucrose, PEG 4000, HEPES, CoCl2, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 1.80 Å
1C22 E. COLI METHIONINE AMINOPEPTIDASE: TRIFLUOROMETHIONINE COMPLEX Deposited 1999-07-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–264（263 aa）
Mutation：R175Q CO COBALT (II) ION × 2 NA SODIUM ION × 1 MF3 2-AMINO-4-TRIFLUOROMETHYLSULFANYL-BUTYRIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；HEPES, CoCl2, K2SO4, Methionine, PEG4000, NaCl, N-octanoyl sucrose, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 1.75 Å
1C23 E. COLI METHIONINE AMINOPEPTIDASE: METHIONINE PHOSPHONATE COMPLEX Deposited 1999-07-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–264（263 aa）
Mutation：R175Q CO COBALT (II) ION × 2 NA SODIUM ION × 1 MPH (1-AMINO-3-METHYLSULFANYL-PROPYL)-PHOSPHONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；Hepes, NaCl, K2SO4, CoCl2, PEG 4000, methionine, N-octanoyl sucrose, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.00 Å
1C24 E. COLI METHIONINE AMINOPEPTIDASE: METHIONINE PHOSPHINATE COMPLEX Deposited 1999-07-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–264（263 aa） Fragment：METHIONINE PHOSPHINATE
Mutation：R175Q CO COBALT (II) ION × 2 NA SODIUM ION × 1 MPJ (1-AMINO-3-METHYLSULFANYL-PROPYL)-PHOSPHINIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；Hepes, NaCl, CoCl2, K2SO4, PEG 4000, N-octanoyl sucrose, methionine, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 1.70 Å
1C27 E. COLI METHIONINE AMINOPEPTIDASE:NORLEUCINE PHOSPHONATE COMPLEX Deposited 1999-07-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–264（263 aa） Fragment：NORLEUCINE PHOSPHONATE
Mutation：R175Q CO COBALT (II) ION × 2 NA SODIUM ION × 1 NLP (1-AMINO-PENTYL)-PHOSPHONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；Hepes, NaCl, CoCl2, K2SO4, methionine, N-octanoyl sucrose, PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 1.95 Å
1MAT STRUCTURE OF THE COBALT-DEPENDENT METHIONINE AMINOPEPTIDASE FROM ESCHERICHIA COLI: A NEW TYPE OF PROTEOLYTIC ENZYME Deposited 1992-12-02 Different mutation/modification 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 × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.40 Å
1XNZ Crystal Structure of Mn(II) form of E. coli. Methionine Aminopeptidase in complex with 5-(2-chlorophenyl)furan-2-carboxylic acid Deposited 2004-10-05 Different mutation/modification 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 FCD 5-(2-CHLOROPHENYL)FURAN-2-CARBOXYLIC 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 1.52 Å R-free 0.250
2BB7 Mn Form Of E. coli Methionine Aminopeptidase In Complex With a quinolinyl sulfonamide inhibitor Deposited 2005-10-17 Different mutation/modification 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 × 3 NA SODIUM ION × 1 QMS N-(QUINOLIN-8-YL)METHANESULFONAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；PEG 20000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.70 Å R-free 0.233
2MAT E.COLI METHIONINE AMINOPEPTIDASE AT 1.9 ANGSTROM RESOLUTION Deposited 1999-03-29 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）
Mutation：R175Q CO COBALT (II) ION × 3 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.1；CRYSTALS OF THE CO(II)-SUBSTITUTED ENZYME WERE GROWN AT ROOM TEMPERATURE BY VAPOR DIFFUSION IN 20-30 UL SITTING DROPS AFTER MIXING THE PROTEIN, 12 MG/ML SOLUTION IN STORAGE BUFFER(25 MM HEPES PH 6.8, 25 MM K2SO4, 100 MM NACL, 1 MM COCL2, 15 MM METHIONINE),CONTAINING 48.8 MM N-OCTANOYL SUCROSE, 1:1 WITH WELL SOLUTIONS (24-26% PEG4000, 0.1M HEPES PH7.0-7.2,FRESH 2 MM COCL2)., pH 7.1, VAPOR DIFFUSION, HANGING DROP
Resolution 1.90 Å
3MAT E.COLI METHIONINE AMINOPEPTIDASE TRANSITION-STATE INHIBITOR COMPLEX Deposited 1999-03-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–264（264 aa）
Mutation：R175Q CO COBALT (II) ION × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.1；CRYSTALS OF THE CO(II)-SUBSTITUTED ENZYME WERE GROWN AT ROOM TEMPERATURE BY VAPOR DIFFUSION IN 20-30 UL SITTING DROPS AFTER MIXING THE PROTEIN, 12 MG/ML SOLUTION IN STORAGE BUFFER(25 MM HEPES PH 6.8, 25 MM K2SO4, 100 MM NACL, 1 MM COCL2, 15 MM METHIONINE),CONTAINING 48.8 MM N-OCTANOYL SUCROSE, 1:1 WITH WELL SOLUTIONS (24-26% PEG4000, 0.1M HEPES PH7.0-7.2,FRESH 2 MM COCL2). CRYSTALS WERE OBTAINED OF THE INHIBITOR COMPLEX BY INCUBATING THE PROTEIN AS ABOVE AT ROOM TEMPERATURE FOR 5 MIN WITH A 20-FOLD MOLAR EXCESS OF THE INHIBITOR DISSOLVED IN DMSO. THE FINAL INHIBITOR:ENZYME RATIO WAS 10:1 (1% DMSO) AFTER MIXING THE PREFORMED COMPLEX WITH WELL SOLUTION (0.1M MES PH 6.1,
Resolution 2.00 Å
4MAT E.COLI METHIONINE AMINOPEPTIDASE HIS79ALA MUTANT Deposited 1999-03-29 Different mutation/modification 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）
Mutation：R175Q, H79A NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；Crystals of the HIS79ALA mutant were obtained by mixing the apoenzyme retaining the C-terminal HISs-tag (6.7 mg/ml, 20 mM DTT, 25 mM HEPES pH 6.8, 25 mM K2SO4, 100 mM NaCl) with an equal volume of well solution (22-27 % PEG 3400, 0.1 M HEPES pH 7.0, 200 mM NaCl). Diffraction quality crystals were obtained after macroseeding into 20 uL hanging drops.
Resolution 2.00 Å

11 other PDB entries and 11 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 1–264； UniProt 1–264

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

SAXS profile for 1yvm

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1yvm
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1yvm
Deposition date deposition_date2005-02-16
Structure title titleE. coli Methionine Aminopeptidase in complex with thiabendazole
Keywords keywordsHYDROLASE(ALPHA-AMINOACYLPEPTIDE), METAL COMPLEX, THIABENDAZOLE, METHIONINE AMINOPEPTIDASE, INHIBITOR, Hydrolase; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier18.31 Å
Radius of gyration Rg (electron density) rg_electron17.35 Å
Forward intensity I(0) i015575700.00
Molecular weight molecular_weight29477.0 kDa
Excluded volume excluded_volume36746 ų
Envelope volume envelope_volume40608 ų
Hydration-shell volume shell_volume19032 ų
Envelope diameter envelope_diameter58.7 Å
Shell Rg shell_rg24.11 Å
Envelope Rg envelope_rg17.75 Å
Shape Rg shape_rg17.36 Å
Total Rg total_rg18.28 Å
Total atoms total_atoms2051
Residues n_residues262
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax57.8 Å
Rg (real space) rg_real18.20 Å
Rg uncertainty (real space) rg_real_error0.28 Å
I(0) (real space) i0_real1.5580e+07
I(0) uncertainty (real space) i0_real_error1.9350e+05
Rg (reciprocal space) rg_reciprocal18.22 Å
I(0) (reciprocal space) i0_reciprocal15580000.0000
Solution quality estimate total_estimate0.8922
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.6 Å
Skewness Skewness skewness0.169
Kurtosis Kurtosis kurtosis-0.404
Angular range angular_range— – 0.4350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4336000.0000
Real-space data points n_real_points75
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.875; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.984
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1yvma_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.127 — Creatinase/aminopeptidase
Superfamily Superfamily superfamilyd.127.1 — Creatinase/aminopeptidase
Family Family familyd.127.1.1 — Creatinase/aminopeptidase

CATH v4.4 (1 domains)

Domain ID domain_id1yvmA00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology230 — Creatine Amidinohydrolase
Homologous superfamily homologous superfamily10 — Creatinase/methionine aminopeptidase superfamily
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8. Citations (1)

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9. Files and Curves (10)