UniProt O53223
L,D-transpeptidase 2 (O53223)
L,D-transpeptidase 2 (UniProt O53223), EC 2.3.2.-: 51 experimental structures and 1 predicted model on GenesisL1, 16 ligands bound, 82 pockets. Binding sites, druggability and experiment against prediction (TM-score) in GL1X.
- UniProt
- O53223
- Protein
- L,D-transpeptidase 2
- EC
- 2.3.2.-
- Experimental structures
- 51
- Predicted models
- 1
- Ligands
- 16
- Pockets
- 82 · 12 records with a druggable one
Structures
52 records of O53223 in the MolNFT archive: 51 experimental, 1 predicted.
| Entry | Title | Method | Chains | Ligands | Pockets |
|---|---|---|---|---|---|
| 3TUR | Crystal Structure of M. tuberculosis LD-transpeptidase type 2 complexed with a peptidoglycan… | x-ray diffraction | A, B | — | — |
| 3TUR | Crystal structure of M. tuberculosis ld-transpeptidase type 2 complexed with a peptidoglycan… | x-ray diffraction | A, B | — | — |
| 3TX4 | Crystal Structure of Mutant (C354A) M. tuberculosis LD-transpeptidase type 2 | x-ray diffraction | A, B | — | — |
| 3TX4 | Crystal structure of mutant (C354A) M. tuberculosis ld-transpeptidase type 2 | x-ray diffraction | A, B | — | — |
| 3U1P | Crystal Structure of M. tuberculosis LD-transpeptidase type 2 with Modified Catalytic Cysteine… | x-ray diffraction | A, B | — | — |
| 3U1P | Crystal structure of M. tuberculosis ld-transpeptidase type 2 with modified catalytic cysteine… | x-ray diffraction | A, B | — | — |
| 3U1Q | Crystal Structure of M. tuberculosis LD-transpeptidase type 2 with 2-Mercaptoethanol | x-ray diffraction | A, B | — | — |
| 3U1Q | Crystal structure of M. tuberculosis ld-transpeptidase type 2 with 2- mercaptoethanol | x-ray diffraction | A, B | — | — |
| 3VAE | Crystal Structure of M. tuberculosis LD-transpeptidase type 2 with Modified Catalytic Cysteine… | x-ray diffraction | A, B | — | — |
| 3VAE | Crystal structure of M. tuberculosis ld-transpeptidase type 2 with modified catalytic cysteine… | x-ray diffraction | A, B | — | — |
| 3VYN | Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase LdtMt2 N55 truncation mutant… | x-ray diffraction | A, B | — | — |
| 3VYN | Crystal structure of mycobacterium tuberculosis L,D-transpeptidase LDTMT2 N55 truncation mutant… | x-ray diffraction | A, B | — | — |
| 3VYO | Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase LdtMt2 N140 truncation mutant… | x-ray diffraction | A, B | — | — |
| 3VYO | Crystal structure of mycobacterium tuberculosis L,D-transpeptidase LDTMT2 N140 truncation mutant… | x-ray diffraction | A, B | — | — |
| 3VYP | Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase LdtMt2-N140 adduct with meropenem | x-ray diffraction | A, B | — | — |
| 3VYP | Crystal structure of mycobacterium tuberculosis L,D-transpeptidase LDTMT2-N140 adduct with meropenem | x-ray diffraction | A, B | — | — |
| 4GSQ | Structural basis for the inhibition of Mycobacterium tuberculosis L,D-transpeptidase by meropenem… | x-ray diffraction | A | — | — |
| 4GSQ | Structural basis for the inhibition of mycobacterium tuberculosis L,D- transpeptidase by meropenem… | x-ray diffraction | A | — | — |
| 4GSR | Structural basis for the inhibition of Mycobacterium tuberculosis L,D-transpeptidase by meropenem… | x-ray diffraction | A | — | — |
| 4GSR | Structural basis for the inhibition of mycobacterium tuberculosis L,D- transpeptidase by meropenem… | x-ray diffraction | A | — | — |
| 4GSU | Structural basis for the inhibition of Mycobacterium tuberculosis L,D-transpeptidase by meropenem… | x-ray diffraction | A, B | — | — |
| 4GSU | Structural basis for the inhibition of mycobacterium tuberculosis L,D- transpeptidase by meropenem… | x-ray diffraction | A, B | — | — |
| 4HU2 | Crystal structure of LdtMt2, a L,D-transpeptidase from Mycobacterium tuberculosis: domain A and B | x-ray diffraction | A | — | — |
| 4HU2 | Crystal structure of LDTMT2, a L,D-transpeptidase from mycobacterium tuberculosis: domain a and B | x-ray diffraction | A | — | — |
| 4HUC | Crystal structure of LdtMt2, a L,D-transpeptidase from Mycobacterium tuberculosis: domain B and C | x-ray diffraction | A, B | — | — |
| 4HUC | Crystal structure of LDTMT2, a L,D-transpeptidase from mycobacterium tuberculosis: domain B and C | x-ray diffraction | A, B | — | — |
| 5D7H | X-ray crystal structure of L,D transpeptidase 2 from mycobacterium tuberculosis | x-ray diffraction | A, B | SO4 | 7 (best 0.71) |
| 5D7H | X-ray crystal structure of L,D transpeptidase 2 from mycobacterium tuberculosis | x-ray diffraction | A, B | — | — |
| 5DC2 | X-ray crystal structure of a enzymatically degraded biapenem-adduct of L,D-transpeptidase 2 from… | x-ray diffraction | A, B | 58U, SO4 | 6 (best 0.70) |
| 5DC2 | X-ray crystal structure of a enzymatically degraded biapenem-adduct of L,D-transpeptidase 2 from… | x-ray diffraction | A, B | — | — |
| 5DCC | X-RAY CRYSTAL STRUCTURE OF a TEBIPENEM ADDUCT OF L,D TRANSPEPTIDASE 2 FROM MYCOBACTERIUM… | x-ray diffraction | A, B | 58U, SO4 | 6 (best 0.72) |
| 5DCC | X-ray crystal structure of a tebipenem adduct of L,D transpeptidase 2 from mycobacterium… | x-ray diffraction | A, B | — | — |
| 5DU7 | Crystal structure of ldtMt2 at 1.79 Angstrom resolution | x-ray diffraction | A, B, D, C | — | — |
| 5DU7 | Crystal structure of LDTMT2 at 1.79 ångström resolution | x-ray diffraction | A, B, D, C | — | — |
| 5DUJ | Crystal structure of ldtMt2 in complex with Faropenem adduct | x-ray diffraction | A, B | SO4, DGF | — |
| 5DUJ | Crystal structure of LDTMT2 in complex with faropenem adduct | x-ray diffraction | A, B | — | — |
| 5LBG | Crystal structure of the Mycobacterium tuberculosis L,D-transpeptidase-2 (LdtMt2) BC-module with… | x-ray diffraction | A, B | 3HL | 5 (best 0.81) |
| 5LBG | Crystal structure of the mycobacterium tuberculosis L,D- transpeptidase-2 (LDTMT2) bc-module with… | x-ray diffraction | A, B | 3HL | — |
| 6RLG | Crystal structure of LdtMt2 from Mycobacterium tuberculosis | x-ray diffraction | A, B | NO3, NA | 7 (best 0.68) |
| 6RLG | Crystal structure of LDTMT2 from mycobacterium tuberculosis | x-ray diffraction | A, B | NO3, NA | — |
| 6RRM | Crystal structure of LdtMt2 from Mycobacterium tuberculosis bound to Ebselen | x-ray diffraction | A, B | NH4, 9JT | 6 (best 0.71) |
| 6RRM | Crystal structure of LDTMT2 from mycobacterium tuberculosis bound to ebselen | x-ray diffraction | A, B | NH4, 9JT | — |
| 8A1J | Crystal structure of the transpeptidase LdtMt2 from Mycobacterium tuberculosis in complex with… | x-ray diffraction | A, B | KSU | 7 (best 0.70) |
| 8A1K | Crystal structure of the transpeptidase LdtMt2 from Mycobacterium tuberculosis in complex with… | x-ray diffraction | A, B | KT6 | 6 (best 0.69) |
| 8A1L | Crystal structure of the transpeptidase LdtMt2 from Mycobacterium tuberculosis in complex with… | x-ray diffraction | A, B | KS9, NA, CL | 6 (best 0.70) |
| 8A1M | Crystal structure of the transpeptidase LdtMt2 from Mycobacterium tuberculosis in complex with… | x-ray diffraction | A, B | KUL, NA, CL | 7 (best 0.69) |
| 8A1O | Crystal structure of the transpeptidase LdtMt2 from Mycobacterium tuberculosis in complex with… | x-ray diffraction | A | KTI, NA, CL | 2 (best 0.47) |
| 8BK3 | Crystal structure of the transpeptidase LdtMt2 from Mycobacterium tuberculosis in complex with… | x-ray diffraction | A, B | QXU, NO3 | 8 (best 0.69) |
| 8J65 | the structure of L,D-transpeptidase LdtMt2 complex with citrate | x-ray diffraction | A, B | — | 6 (best 0.70) |
| 8PXY | Crystal structure of the transpeptidase LdtMt2 C354S mutant from Mycobacterium tuberculosis in… | x-ray diffraction | A | CL | 2 (best 0.48) |
| 8PXZ | Crystal structure of the transpeptidase LdtMt2 from Mycobacterium tuberculosis in complex with… | x-ray diffraction | A | DAL, CL | 1 (best 0.48) |
| O53223 | AlphaFold monomer V2.0 prediction for L,D-transpeptidase 2 (O53223) | predicted | A | — | — |
Ligands
- CL · Chloride ion · in 5 records
- NA · Sodium ion · in 5 records
- SO4 · Sulfate ion · in 4 records
- NO3 · Nitrate ion · in 3 records
- 3HL · (3S)-3-hydroxybutanoic acid · in 2 records
- 58U · (4S)-4-methyl-2,5,7-trioxoheptanoic acid · in 2 records
- 9JT · ~{N}-phenyl-2-selanyl-benzamide · in 2 records
- NH4 · Ammonium ion · in 2 records
- DAL · D-alanine · in 1 record
- DGF · (2R,5R)-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-5-[(2R)-tetrahydrofuran-2-yl]-2,5-dihydro-1,3-thiazole-4-carboxylic acid · in 1 record
- KS9 · (phenylmethyl) N-[(3S,4S)-4-methyl-2-oxidanylidene-hexan-3-yl]carbamate · in 1 record
- KSU · 1-phenylpyrrolidine-2,5-dione · in 1 record
- KT6 · 4,5-bis(chloranyl)-N-(2-hydroxyethyl)-2-sulfanyl-benzamide · in 1 record
- KTI · (E)-3-chloranyl-3-[(2-chlorophenyl)methylsulfonyl]-N-(5-methoxypyridin-2-yl)prop-2-enamide · in 1 record
- KUL · 1-(2-fluoranyl-5-methylsulfonyl-phenyl)pyrrolidine-2,5-dione · in 1 record
- QXU · 1-[(2~{S},3~{R})-3-phenyloxiran-2-yl]ethanone · in 1 record
Experiment against prediction
- 5DUJ chain A against the predicted model O53223: TM-score 1.00, RMSD 0.27 Å
- 5DUJ chain A against the predicted model O53223: TM-score 1.00, RMSD 0.27 Å
- 5DU7 chain A against the predicted model O53223: TM-score 1.00, RMSD 0.26 Å
- 5DU7 chain A against the predicted model O53223: TM-score 1.00, RMSD 0.26 Å
- 5DU7 chain C against the predicted model O53223: TM-score 1.00, RMSD 0.28 Å
- 5DU7 chain C against the predicted model O53223: TM-score 1.00, RMSD 0.28 Å
- 5DCC chain B against the predicted model O53223: TM-score 1.00, RMSD 0.31 Å
- 5DCC chain B against the predicted model O53223: TM-score 1.00, RMSD 0.31 Å
- 5DC2 chain B against the predicted model O53223: TM-score 1.00, RMSD 0.32 Å
- 5DC2 chain B against the predicted model O53223: TM-score 1.00, RMSD 0.32 Å
Elsewhere
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