Download MendeleyCrystal structure of Entamoeba histolytica methionine gamma-lyase 1
Karaki, T., Sato, D., Shimizu, A., Nozaki, T., Harada, S.To be published.
3AEM
Reaction intermediate structure of Entamoeba histolytica methionine gamma-lyase 1 containing Michaelis complex and methionine imine-pyridoxamine-5'-phosphate
- PDB DOI: https://doi.org/10.2210/pdb3AEM/pdb
- Classification: LYASE
- Organism(s): Entamoeba histolytica
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2010-02-10 Released: 2011-02-09
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.196
- R-Value Work: 0.151
- R-Value Observed: 0.153
Starting Model: experimental
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This is version 1.4 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Methionine gamma-lyase | 389 | Entamoeba histolytica | Mutation(s): 0 Gene Names: metg EC: 4.4.1.11 |  | |
UniProt | |||||
Find proteins for Q86D28 (Entamoeba histolytica) Explore Q86D28 Go to UniProtKB: Q86D28 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q86D28 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Methionine gamma-lyase | 389 | Entamoeba histolytica | Mutation(s): 0 Gene Names: metg EC: 4.4.1.11 |  | |
UniProt | |||||
Find proteins for Q86D28 (Entamoeba histolytica) Explore Q86D28 Go to UniProtKB: Q86D28 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q86D28 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 2LM Query on 2LM | E [auth A], H [auth B], M [auth D] | (2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]-4-(methylsulfanyl)butanoic acid C13 H19 N2 O7 P S RNHGWTJOZCEIDD-RVDMUPIBSA-N |  | ||
| MET Query on MET | J [auth C] | METHIONINE C5 H11 N O2 S FFEARJCKVFRZRR-BYPYZUCNSA-N |  | ||
| SO4 Query on SO4 | F [auth A], I [auth B], K [auth C], N [auth D] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| GOL Query on GOL | G [auth A], L [auth C] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| LLP Query on LLP | C | L-PEPTIDE LINKING | C14 H22 N3 O7 P |  | LYS |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.196
- R-Value Work: 0.151
- R-Value Observed: 0.153
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 99.086 | α = 90 |
| b = 85.332 | β = 101.9 |
| c = 114.331 | γ = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| MOLREP | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| HKL-2000 | data collection |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
Entry History
Deposition Data
- Released Date: 2011-02-09 Deposition Author(s): Karaki, T., Sato, D., Shimizu, A., Nozaki, T., Harada, S.
Revision History (Full details and data files)
- Version 1.0: 2011-02-09
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2017-10-11
Changes: Refinement description - Version 1.3: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description - Version 1.4: 2023-11-15
Changes: Data collection
