MolNFT v1 · #111019 · protein
The crystal structure of a peptidoglycan synthetase from bifidobacterium adolescentis atcc 15703
4YE5 · Peptidoglycan synthetase penicillin-binding protein 3: “The crystal structure of a peptidoglycan synthetase from bifidobacterium adolescentis atcc 15703”. X-ray diffraction, 15 pockets (best druggability 0.66). MolNFT v1 #111019 on…
- PDB
- 4YE5
- Type
- protein
- Length
- 1,080 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidoglycan synthetase penicillin-binding protein 3
- UniProt
- A1A2F5
- Pockets
- 15 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidoglycan synthetase penicillin-binding protein 3 | protein | 546 | 31% helix, 24% strand | A1A2F5 |
| B | Peptidoglycan synthetase penicillin-binding protein 3 | protein | 534 | 31% helix, 22% strand | A1A2F5 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 412 | 0.66 | 0.79 | 55 | empty |
| 2 | 63 | 0.63 | 0.92 | 14 | empty |
| 3 | 326 | 0.60 | 0.78 | 47 | empty |
| 4 | 323 | 0.59 | 0.77 | 47 | empty |
| 5 | 212 | 0.48 | 0.75 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 764 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified, 2 disulfide (engineered, disulfide).
Compared structures
- 4YE5 · The crystal structure of a peptidoglycan synthetase from Bifidobacterium adolescentis… · the same entry in another collection · 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 A1A2F5
- Elsewhere: RCSB PDB 4YE5 · PDBe 4YE5 · UniProt A1A2F5
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