MolNFT v1 · #54957 · protein
Unexpected tricovalent binding mode of boronic acids within the active site of a penicillin binding protein
2Y59 · D-alanyl-D-alanine carboxypeptidase: “Unexpected tricovalent binding mode of boronic acids within the active site of a penicillin binding protein”. X-ray diffraction, 3 ligands (ZA3, MG, SO4), 9 pockets (best druggability 0.66).…
- PDB
- 2Y59
- Type
- protein
- Length
- 1,862 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-alanyl-D-alanine carboxypeptidase
- EC
- 3.4.16.4
- UniProt
- P39045
- Ligands
- ZA3, MG, SO4
- Pockets
- 9 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | D-alanyl-D-alanine carboxypeptidase (EC 3.4.16.4) | protein | 466 | 32% helix, 24% strand | P39045 |
| B, C | D-alanyl-D-alanine carboxypeptidase (EC 3.4.16.4) | protein | 465 | 31% helix, 23% strand | P39045 |
Ligands and binding sites
- ZA3 · Trihydroxy-[[(2-nitrophenyl)carbonylamino]methyl]boron · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, D
- SO4 · Sulfate ion · ion · 21 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 911 | 0.66 | 0.73 | 70 | SO4 |
| 2 | 307 | 0.60 | 0.78 | 42 | empty |
| 3 | 235 | 0.52 | 0.76 | 41 | ZA3 |
| 4 | 203 | 0.50 | 0.76 | 34 | ZA3 |
| 5 | 56 | 0.45 | 0.84 | 19 | empty |
Interfaces
3 interfaces between chains.
- B–D · 439 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 376 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 144 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 2Y59 · Unexpected tricovalent binding mode of boronic acids within the active site of a… · the same entry in another collection · chain D against D, TM-score 1.00
- P39045 · AlphaFold monomer V2.0 prediction for D-alanyl-D-alanine carboxypeptidase (P39045) · a predicted model of the same protein · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P39045
- Elsewhere: RCSB PDB 2Y59 · PDBe 2Y59 · UniProt P39045
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