MolNFT v1 · #135407 · protein
Crystal structure of wild-type S. aureus penicillin binding protein 4 (PBP4) in complex with nafcillin
5TY7 · Penicillin-binding protein 4: “Crystal structure of wild-type S. aureus penicillin binding protein 4 (PBP4) in complex with nafcillin”. X-ray diffraction, 3 ligands (NFF, ZN, NA), 4 pockets (best druggability 0.71). MolNFT v1…
- PDB
- 5TY7
- Type
- protein
- Length
- 713 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein 4
- UniProt
- A0A0H2WY27
- Ligands
- NFF, ZN, NA
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 4 | protein | 355 | 34% helix, 26% strand | A0A0H2WY27 |
| B | Penicillin-binding protein 4 | protein | 358 | 33% helix, 26% strand | A0A0H2WY27 |
Ligands and binding sites
- NFF · (2R,4S)-2-[(1R)-1-{[(2-ethoxynaphthalen-1-yl)carbonyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 755 | 0.71 | 0.77 | 59 | empty |
| 2 | 255 | 0.57 | 0.78 | 47 | NFF |
| 3 | 247 | 0.53 | 0.77 | 39 | NFF |
| 4 | 59 | 0.27 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 189 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5TY7 · Crystal structure of wild-type S. aureus penicillin binding protein 4 (PBP4) in complex… · 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 A0A0H2WY27
- Elsewhere: RCSB PDB 5TY7 · PDBe 5TY7 · UniProt A0A0H2WY27
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