UniProt I6Y9J2
L,D-transpeptidase 2 (I6Y9J2)
L,D-transpeptidase 2 (UniProt I6Y9J2), EC 2.3.2.-: 36 experimental structures and 1 predicted model on GenesisL1, 20 ligands bound, 22 pockets. Binding sites, druggability and experiment against prediction (TM-score) in GL1X.
- UniProt
- I6Y9J2
- Protein
- L,D-transpeptidase 2
- EC
- 2.3.2.-
- Experimental structures
- 36
- Predicted models
- 1
- Ligands
- 20
- Pockets
- 22 · 5 records with a druggable one
Structures
37 records of I6Y9J2 in the MolNFT archive: 36 experimental, 1 predicted.
| Entry | Title | Method | Chains | Ligands | Pockets |
|---|---|---|---|---|---|
| 4QR7 | Structure and specificity of L-D-Transpeptidase from Mycobacterium tuberculosis and antibiotic… | x-ray diffraction | A | — | — |
| 4QR7 | Structure and specificity of L-D-transpeptidase from mycobacterium tuberculosis and antibiotic… | x-ray diffraction | A | — | — |
| 4QRA | Structure and specificity of L-D-Transpeptidase from Mycobacterium tuberculosis and antibiotic… | x-ray diffraction | A, B | — | — |
| 4QRA | Structure and specificity of L-D-transpeptidase from mycobacterium tuberculosis and antibiotic… | x-ray diffraction | A, B | — | — |
| 4QRB | Structure and specificity of L-D-Transpeptidase from Mycobacterium tuberculosis and antibiotic… | x-ray diffraction | A | — | — |
| 4QRB | Structure and specificity of L-D-transpeptidase from mycobacterium tuberculosis and antibiotic… | x-ray diffraction | A | — | — |
| 4QTF | Structure and specificity of L-D-Transpeptidase from Mycobacterium tuberculosis and antibiotic… | x-ray diffraction | A | — | — |
| 4QTF | Structure and specificity of L-D-transpeptidase from mycobacterium tuberculosis and antibiotic… | x-ray diffraction | A | — | — |
| 5DVP | Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase 2 with Doripenem adduct | x-ray diffraction | A, B | DRW, SO4, POA | — |
| 5DVP | Crystal structure of mycobacterium tuberculosis L,D-transpeptidase 2 with doripenem adduct | x-ray diffraction | A, B | — | — |
| 5DZJ | Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase 2 with carbapenem drug T206 in… | x-ray diffraction | A, B | 6B7 | 6 (best 0.51) |
| 5DZJ | Crystal structure of mycobacterium tuberculosis L,D-transpeptidase 2 with carbapenem drug T206 in… | x-ray diffraction | A, B | — | — |
| 5DZP | Crystal structure of mycobacterium tuberculosis L,D-transpeptidase 2 with carbapenem drug T206 in… | x-ray diffraction | A, B | — | — |
| 5E1G | Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase 2 with carbapenem drug T208 | x-ray diffraction | A, B | T8G | — |
| 5E1G | Crystal structure of mycobacterium tuberculosis L,D-transpeptidase 2 with carbapenem drug T208 | x-ray diffraction | A, B | — | — |
| 5E1I | Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase 2 with carbapenem drug T210 | x-ray diffraction | A, B | NA, 6B8 | — |
| 5E1I | Crystal structure of mycobacterium tuberculosis L,D-transpeptidase 2 with carbapenem drug T210 | x-ray diffraction | A, B | — | — |
| 5K69 | Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase 2 with carbapenem drug T224 | x-ray diffraction | A, B | 6QR | 6 (best 0.72) |
| 5K69 | Crystal structure of mycobacterium tuberculosis L,D-transpeptidase 2 with carbapenem drug T224 | x-ray diffraction | A, B | 6QR | — |
| 5LB1 | Crystal structure of the Mycobacterium tuberculosis L,D-transpeptidase-2 (LdtMt2) BC-module with… | x-ray diffraction | A, B | MNB | 2 (best 0.77) |
| 5LB1 | Crystal structure of the mycobacterium tuberculosis L,D- transpeptidase-2 (LDTMT2) bc-module with… | x-ray diffraction | A, B | MNB | — |
| 6IYV | Crystal sturucture of L,D-transpeptidase LdtMt2 from Mycobacterium tuberculosis in complex with… | x-ray diffraction | B, A | SO4 | — |
| 6IYV | Crystal sturucture of L,D-transpeptidase LDTMT2 from mycobacterium tuberculosis in complex with… | x-ray diffraction | B, A | SO4 | — |
| 6IYW | Crystal sturucture of L,D-transpeptidase LDTMT2 from mycobacterium tuberculosis in complex with… | x-ray diffraction | A, B, C, D, E, F | IM2 | — |
| 6LQB | A third intermediate state of L,D-transpeptidase LdtMt2-ertapenem adduct | x-ray diffraction | A, B | — | — |
| 6LQB | A third intermediate state of L,D-transpeptidase LDTMT2-ertapenem adduct | x-ray diffraction | A, B | — | — |
| 7A0Z | Lpps with covalent adduct derived from 1B | x-ray diffraction | A, B | BT6, TAM | — |
| 7A10 | Lpps with covalent adduct derived from 1G | x-ray diffraction | A, B | QU5 | — |
| 7A11 | LppS with covalent adduct derived from 1E | x-ray diffraction | A, B | XL3 | 4 (best 0.80) |
| 7A11 | Lpps with covalent adduct derived from 1E | x-ray diffraction | A, B | XL3 | — |
| 7A1C | LDTMT2 with covalent adduct derived from N-thio-beta-lactam 1A | x-ray diffraction | A, B | — | — |
| 7A1E | LppS with covalent adduct derived from 1c | x-ray diffraction | A, B | SDQ | 4 (best 0.81) |
| 7A1E | Lpps with covalent adduct derived from 1C | x-ray diffraction | A, B | SDQ | — |
| 7F71 | Crystal structure of the mycobacterium tuberculosis L,D- transpeptidase-2 (LDTMT2) with… | x-ray diffraction | A, B | BGC | — |
| 7F8P | Crystal structure of the mycobacterium tuberculosis L,D- transpeptidase-2 (LDTMT2) with new… | x-ray diffraction | A, B | 59I, 56X | — |
| 7KEM | Crystallographic structure of L,D-transpeptidase 2 from mycobacterium tuberculosis | x-ray diffraction | A, B | 0JC, PT | — |
| I6Y9J2 | AlphaFold monomer V2.0 prediction for L,D-transpeptidase 2 (I6Y9J2) | predicted | A | — | — |
Ligands
- SO4 · Sulfate ion · in 3 records
- 6QR · (2~{S},3~{R},4~{R})-4-(1~{H}-indol-3-ylsulfanyl)-3-methyl-2-[(2~{S},3~{S})-3-oxidanyl-1-oxidanylidene-butan-2-yl]-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid · in 2 records
- MNB · 5-mercapto-2-nitro-benzoic acid · in 2 records
- SDQ · phenylmethanethiol · in 2 records
- XL3 · propane-1-thiol · in 2 records
- 0JC · Di-mu-iodobis(ethylenediamine)diplatinum(ii) · in 1 record
- 56X · (4R,5S,6S)-6-((R)-1-hydroxyethyl)-3-((2-isopropoxy-2-oxoethyl)thio)-4-methyl-7-oxo-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid · in 1 record
- 59I · (2R,3R)-3-methyl-4-(2-oxidanylidene-2-propan-2-yloxy-ethyl)sulfanyl-2-[(2R)-3-oxidanyl-1-oxidanylidene-butan-2-yl]-2,3-dihydro-1H-pyrrole-5-carboxylic acid · in 1 record
- 6B7 · (2~{R},3~{R},4~{R})-4-methyl-3-(2-oxidanylidene-2-propoxy-ethyl)sulfanyl-5-[(2~{S},3~{R})-3-oxidanyl-1-oxidanylidene-butan-2-yl]-3,4-dihydro-2~{H}-pyrrole-2-carboxylic acid · in 1 record
- 6B8 · (2S,3R,4R)-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-4-(methylsulfanyl)-3,4-dihydro-2H-pyrrole-5-carboxylic acid · in 1 record
- BGC · beta-D-glucopyranose · in 1 record
- BT6 · Benzenethiol · in 1 record
- DRW · (2S,3R,4S)-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-4-({(3S,5S)-5-[(sulfamoylamino)methyl]pyrrolidin-3-yl}sulfanyl)-3,4-dihydro-2H-pyrrole-5-carboxylic acid · in 1 record
- IM2 · (5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carbox ylic acid · in 1 record
- NA · Sodium ion · in 1 record
- POA · Phosphonoacetaldehyde · in 1 record
- PT · Platinum (II) ion · in 1 record
- QU5 · 4-methoxycyclohexa-2,5-diene-1-thione · in 1 record
- T8G · (2~{S},3~{R},4~{R})-4-(2-cyclohexyloxy-2-oxidanylidene-ethyl)sulfanyl-3-methyl-2-[(2~{S},3~{R})-3-oxidanyl-1-oxidanylidene-butan-2-yl]-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid · in 1 record
- TAM · Tris(hydroxyethyl)aminomethane · in 1 record
Experiment against prediction
- 5K69 chain A against the predicted model I6Y9J2: TM-score 1.00, RMSD 0.32 Å
- 5K69 chain A against the predicted model I6Y9J2: TM-score 1.00, RMSD 0.32 Å
- 5DZJ chain A against the predicted model I6Y9J2: TM-score 1.00, RMSD 0.35 Å
- 5E1I chain A against the predicted model I6Y9J2: TM-score 1.00, RMSD 0.36 Å
- 5E1I chain A against the predicted model I6Y9J2: TM-score 1.00, RMSD 0.36 Å
- 5E1G chain A against the predicted model I6Y9J2: TM-score 1.00, RMSD 0.36 Å
- 5E1G chain A against the predicted model I6Y9J2: TM-score 1.00, RMSD 0.36 Å
- 7A1C chain B against the predicted model I6Y9J2: TM-score 1.00, RMSD 0.39 Å
- 7F71 chain A against the predicted model I6Y9J2: TM-score 1.00, RMSD 0.31 Å
- 5DVP chain A against the predicted model I6Y9J2: TM-score 0.99, RMSD 0.49 Å
Elsewhere
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