UniProt P39045
D-alanyl-D-alanine carboxypeptidase (P39045)
D-alanyl-D-alanine carboxypeptidase (UniProt P39045), EC 3.4.16.4: 36 experimental structures and 1 predicted model on GenesisL1, 20 ligands bound, 310 pockets. Binding sites, druggability and experiment against prediction…
- UniProt
- P39045
- Protein
- D-alanyl-D-alanine carboxypeptidase
- EC
- 3.4.16.4
- Experimental structures
- 36
- Predicted models
- 1
- Ligands
- 20
- Pockets
- 310 · 36 records with a druggable one
Structures
37 records of P39045 in the MolNFT archive: 36 experimental, 1 predicted.
| Entry | Title | Method | Chains | Ligands | Pockets |
|---|---|---|---|---|---|
| 1W79 | Crystal structure of the DD-transpeptidase-carboxypeptidase from Actinomadura R39 | x-ray diffraction | A, B, C, D | SO4, MG | 7 (best 0.61) |
| 1W79 | Crystal structure of the dd-transpeptidase-carboxypeptidase from actinomadura R39 | x-ray diffraction | A, B, C, D | SO4, MG | 7 (best 0.61) |
| 1W8Q | Crystal Structure of the DD-Transpeptidase-carboxypeptidase from Actinomadura R39 | x-ray diffraction | A, B, C, D | SO4, CO | 8 (best 0.62) |
| 1W8Q | Crystal structure of the dd-transpeptidase-carboxypeptidase from actinomadura R39 | x-ray diffraction | A, B, C, D | SO4, CO | 8 (best 0.62) |
| 1W8Y | Crystal structure of the nitrocefin acyl-DD-peptidase from Actinomadura R39. | x-ray diffraction | A, B, C, D | SO4, MG, NCF | 9 (best 0.57) |
| 1W8Y | Crystal structure of the nitrocefin acyl-dd-peptidase from actinomadura R39. | x-ray diffraction | A, B, C, D | SO4, MG, NCF | 9 (best 0.57) |
| 2VGJ | Crystal structure of Actinomadura R39 DD-peptidase complexed with a peptidoglycan-mimetic… | x-ray diffraction | A, B, C, D | REC, SO4, MG | 8 (best 0.64) |
| 2VGJ | Crystal structure of actinomadura R39 dd-peptidase complexed with a peptidoglycan-mimetic… | x-ray diffraction | A, B, C, D | REC, SO4, MG | 8 (best 0.64) |
| 2VGK | Crystal structure of Actinomadura R39 DD-peptidase complexed with a peptidoglycan-mimetic… | x-ray diffraction | A, B, C, D | REZ, SO4, MG | 8 (best 0.67) |
| 2VGK | Crystal structure of actinomadura R39 dd-peptidase complexed with a peptidoglycan-mimetic… | x-ray diffraction | A, B, C, D | REZ, SO4, MG | 8 (best 0.67) |
| 2WKE | Crystal structure of the Actinomadura R39 DD-peptidase inhibited by 6- beta-iodopenicillanate. | x-ray diffraction | A, B, C, D | BIY, SO4, CO | 9 (best 0.65) |
| 2WKE | Crystal structure of the actinomadura R39 dd-peptidase inhibited by 6-beta-iodopenicillanate. | x-ray diffraction | A, B, C, D | BIY, SO4, CO | 9 (best 0.65) |
| 2XDM | Crystal structure of a complex between Actinomadura R39 DD peptidase and a peptidoglycan mimetic… | x-ray diffraction | A, B, C, D | SO4, CO, BO8 | 9 (best 0.68) |
| 2XDM | Crystal structure of a complex between actinomadura R39 dd peptidase and a peptidoglycan mimetic… | x-ray diffraction | A, B, C, D | SO4, CO, BO8 | 9 (best 0.68) |
| 2XK1 | Crystal structure of a complex between Actinomadura R39 DD-peptidase and a boronate inhibitor | x-ray diffraction | A, B, C, D | EWB, SO4, CO | 13 (best 0.81) |
| 2XK1 | Crystal structure of a complex between actinomadura R39 dd- peptidase and a boronate inhibitor | x-ray diffraction | A, B, C, D | EWB, SO4, CO | 13 (best 0.81) |
| 2XLN | Crystal structure of a complex between Actinomadura R39 DD-peptidase and a boronate inhibitor | x-ray diffraction | A, B, C, D | EWA, SO4, CO | 8 (best 0.69) |
| 2XLN | Crystal structure of a complex between actinomadura R39 dd-peptidase and a boronate inhibitor | x-ray diffraction | A, B, C, D | EWA, SO4, CO | 8 (best 0.69) |
| 2Y4A | Unexpected tricovalent binding mode of boronic acids within the active site of a penicillin binding… | x-ray diffraction | A, B, C, D | BH6, SO4, MG | 6 (best 0.69) |
| 2Y4A | Unexpected tricovalent binding mode of boronic acids within the active site of a penicillin binding… | x-ray diffraction | A, B, C, D | BH6, SO4, MG | 6 (best 0.69) |
| 2Y55 | Unexpected tricovalent binding mode of boronic acids within the active site of a penicillin binding… | x-ray diffraction | A, B, C, D | FP5, SO4, MG, ACN | 8 (best 0.61) |
| 2Y55 | Unexpected tricovalent binding mode of boronic acids within the active site of a penicillin binding… | x-ray diffraction | A, B, C, D | FP5, SO4, MG, ACN | 8 (best 0.61) |
| 2Y59 | Unexpected tricovalent binding mode of boronic acids within the active site of a penicillin binding… | x-ray diffraction | A, B, C, D | ZA3, SO4, MG | 9 (best 0.66) |
| 2Y59 | Unexpected tricovalent binding mode of boronic acids within the active site of a penicillin binding… | x-ray diffraction | A, B, C, D | ZA3, SO4, MG | 9 (best 0.66) |
| 3ZCZ | Crystal structure of a complex between Actinomadura R39 DD-peptidase and a trifluoroketone inhibitor | x-ray diffraction | A, B, C, D | TFR, SO4, MG | 8 (best 0.69) |
| 3ZCZ | Crystal structure of a complex between actinomadura R39 dd- peptidase and a trifluoroketone… | x-ray diffraction | A, B, C, D | TFR, SO4, MG | 8 (best 0.69) |
| 3ZVT | Unexpected tricovalent binding mode of boronic acids within the active site of a penicillin binding… | x-ray diffraction | A, B, C, D | B07, SO4, MG | 9 (best 0.63) |
| 3ZVT | Unexpected tricovalent binding mode of boronic acids within the active site of a penicillin binding… | x-ray diffraction | A, B, C, D | B07, SO4, MG | 9 (best 0.63) |
| 3ZVW | Unexpected tricovalent binding mode of boronic acids within the active site of a penicillin binding… | x-ray diffraction | A, B, C, D | SO4, MG, FP5, ACN, 33D | 9 (best 0.69) |
| 3ZVW | Unexpected tricovalent binding mode of boronic acids within the active site of a penicillin binding… | x-ray diffraction | A, B, C, D | SO4, MG, FP5, ACN, 33D | 9 (best 0.69) |
| 4B4X | Crystal structure of a complex between Actinomadura R39 DD-peptidase and a sulfonamide boronate… | x-ray diffraction | A, B, C, D | HQZ, SO4, MG | 10 (best 0.68) |
| 4B4X | Crystal structure of a complex between actinomadura R39 dd- peptidase and a sulfonamide boronate… | x-ray diffraction | A, B, C, D | HQZ, SO4, MG | 10 (best 0.68) |
| 4B4Z | Crystal structure of a complex between Actinomadura R39 DD-peptidase and a sulfonamide boronate… | x-ray diffraction | A, B, C, D | BSF, MG, SO4 | 8 (best 0.66) |
| 4B4Z | Crystal structure of a complex between actinomadura R39 dd-peptidase and a sulfonamide boronate… | x-ray diffraction | A, B, C, D | BSF, MG, SO4 | 8 (best 0.66) |
| 4BEN | R39-imipenem Acyl-enzyme crystal structure | x-ray diffraction | A, B, C, D | IM2, MG, SO4 | 9 (best 0.68) |
| 4BEN | R39-imipenem acyl-enzyme crystal structure | x-ray diffraction | A, B, C, D | IM2, MG, SO4 | 9 (best 0.68) |
| P39045 | AlphaFold monomer V2.0 prediction for D-alanyl-D-alanine carboxypeptidase (P39045) | predicted | A | — | — |
Ligands
- SO4 · Sulfate ion · in 36 records
- MG · Magnesium ion · in 26 records
- CO · Cobalt (II) ion · in 10 records
- ACN · Acetone · in 4 records
- FP5 · Phenylacetamidomethyl boronic acid · in 4 records
- 33D · 3,3-dimethylbutan-1-ol · in 2 records
- B07 · 2,6 dimethoxybenzamidoboronic acid · in 2 records
- BH6 · {[(2-chlorobenzoyl)amino]methyl}boronic acid · in 2 records
- BIY · (3S)-2,2-dimethyl-3,4-dihydro-2H-1,4-thiazine-3,6-dicarboxylic acid · in 2 records
- BO8 · (D-alpha-aminopimelylamino)-D-1-ethylboronic acid · in 2 records
- BSF · {[(benzylsulfonyl)amino]methyl}boronic acid · in 2 records
- EWA · [(1S)-1-{[(2,6-dimethoxyphenyl)carbonyl]amino}ethyl]boronic acid · in 2 records
- EWB · [(1S)-1-{[(2-benzylphenyl)carbonyl]amino}ethyl](trihydroxy)borate(1-) · in 2 records
- HQZ · trihydroxy{(1S)-1-[(methylsulfonyl)amino]ethyl}borate(1-) · in 2 records
- 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 2 records
- NCF · (2R)-2-{(1R)-2-oxo-1-[(2-thienylacetyl)amino]ethyl}-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid · in 2 records
- REC · Cephalosporin · in 2 records
- REZ · (2R)-2-amino-7-{[(1R)-1-carboxyethyl]amino}-7-oxoheptanoic acid · in 2 records
- TFR · (2R)-2-amino-7-oxo-7-{[(2R,3S)-4,4,4-trifluoro-3-hydroxybutan-2-yl]amino}heptanoic acid · in 2 records
- ZA3 · Trihydroxy-[[(2-nitrophenyl)carbonylamino]methyl]boron · in 2 records
Experiment against prediction
- 1W79 chain A against the predicted model P39045: TM-score 1.00, RMSD 0.26 Å
- 1W79 chain A against the predicted model P39045: TM-score 1.00, RMSD 0.26 Å
- 2Y59 chain A against the predicted model P39045: TM-score 1.00, RMSD 0.28 Å
- 2Y59 chain A against the predicted model P39045: TM-score 1.00, RMSD 0.28 Å
- 2Y55 chain A against the predicted model P39045: TM-score 1.00, RMSD 0.31 Å
- 2Y55 chain A against the predicted model P39045: TM-score 1.00, RMSD 0.31 Å
- 4BEN chain A against the predicted model P39045: TM-score 1.00, RMSD 0.31 Å
- 4BEN chain A against the predicted model P39045: TM-score 1.00, RMSD 0.31 Å
- 1W8Q chain A against the predicted model P39045: TM-score 1.00, RMSD 0.32 Å
- 1W8Q chain A against the predicted model P39045: TM-score 1.00, RMSD 0.32 Å
Elsewhere
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