MolNFT v1 · #116489 · protein
Crystal structure of penicillin-binding protein 3 in complex with deacylated product of cefoperazone
5DF9 · Cell division protein: “Crystal structure of penicillin-binding protein 3 in complex with deacylated product of cefoperazone”. X-ray diffraction, 2 ligands (59J, SO4), 5 pockets (best druggability 0.65). MolNFT v1 #116489 on…
- PDB
- 5DF9
- Type
- protein
- Length
- 509 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division protein
- EC
- 2.4.1.129
- UniProt
- Q51504
- Ligands
- 59J, SO4
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell division protein (EC 2.4.1.129) | protein | 509 | 34% helix, 26% strand | Q51504 |
Ligands and binding sites
- 59J · (2R,5R)-2-[(R)-carboxy{[(2R)-2-{[(4-ethyl-2,3-dioxopiperazin-1-yl)carbonyl]amino}-2-(4-hydroxyphenyl)acetyl]amino}methyl]-5-methyl-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid · ligand · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 509 | 0.65 | 0.77 | 44 | 59J |
| 2 | 125 | 0.53 | 0.82 | 23 | empty |
| 3 | 68 | 0.40 | 0.80 | 19 | SO4, GOL |
| 4 | 108 | 0.38 | 0.75 | 19 | empty |
| 5 | 90 | 0.36 | 0.76 | 21 | empty |
Compared structures
- 5DF9 · Crystal structure of penicillin-binding protein 3 in complex with deacylated product of… · 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 Q51504
- Elsewhere: RCSB PDB 5DF9 · PDBe 5DF9 · UniProt Q51504
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