MolNFT v1 · #36165 · protein
Crystal structure of penicillin binding protein 4 (dacb) from escherichia COLI, complexed with farom
2EXA · Penicillin-binding protein 4: “Crystal structure of penicillin binding protein 4 (dacb) from escherichia COLI, complexed with farom”. X-ray diffraction, 1 ligand (DGF), 3 pockets (best druggability 0.34). MolNFT v1 #36165 on…
- PDB
- 2EXA
- Type
- protein
- Length
- 443 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein 4
- EC
- 3.4.16.4, 3.4.99.-
- UniProt
- P24228
- Ligands
- DGF
- Pockets
- 3 · best druggability 0.34
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 4 (EC 3.4.16.4, 3.4.99.-) | protein | 443 | 33% helix, 28% strand | P24228 |
Ligands and binding sites
- 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 · ligand · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 54 | 0.34 | 0.77 | 11 | empty |
| 2 | 65 | 0.32 | 0.75 | 17 | DGF |
| 3 | 69 | 0.30 | 0.74 | 17 | empty |
Modifications
Observed in the structure: 2 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 2EXA · Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, complexed… · the same entry in another collection · chain A against A, TM-score 1.00
- P24228 · AlphaFold monomer V2.0 prediction for D-alanyl-D-alanine carboxypeptidase dacb (P24228) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P24228
- Elsewhere: RCSB PDB 2EXA · PDBe 2EXA · UniProt P24228
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