MolNFT v1 · #36163 · protein
Crystal structure of penicillin binding protein 4 (dacb) from escherichia COLI, complexed with penicillin-G
2EX8 · Penicillin-binding protein 4: “Crystal structure of penicillin binding protein 4 (dacb) from escherichia COLI, complexed with penicillin-G”. X-ray diffraction, 1 ligand (PNM), 4 pockets (best druggability 0.40). MolNFT v1 #36163 on…
- PDB
- 2EX8
- Type
- protein
- Length
- 456 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
- PNM
- Pockets
- 4 · best druggability 0.40
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 4 (EC 3.4.16.4, 3.4.99.-) | protein | 456 | 33% helix, 27% strand | P24228 |
Ligands and binding sites
- PNM · Open form - penicillin G · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 99 | 0.40 | 0.76 | 21 | empty |
| 2 | 87 | 0.33 | 0.74 | 21 | empty |
| 3 | 59 | 0.27 | 0.73 | 15 | empty |
| 4 | 58 | 0.24 | 0.72 | 17 | PNM |
Modifications
Observed in the structure: 2 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 2EX8 · 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 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 P24228
- Elsewhere: RCSB PDB 2EX8 · PDBe 2EX8 · UniProt P24228
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