MolNFT v1 · #149439 · protein
Crystal structure of enterococcus faecium D63R penicillin-binding protein 5 (PBP5FM)
6G0K · Low affinity penicillin-binding protein 5 (PBP5): “Crystal structure of enterococcus faecium D63R penicillin-binding protein 5 (PBP5FM)”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.82). MolNFT v1 #149439 on…
- PDB
- 6G0K
- Type
- protein
- Length
- 1,833 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Low affinity penicillin-binding protein 5 (PBP5)
- UniProt
- Q47759
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Low affinity penicillin-binding protein 5 (PBP5) | protein | 629 | 34% helix, 25% strand | Q47759 |
| B | Low affinity penicillin-binding protein 5 (PBP5) | protein | 609 | 33% helix, 27% strand | Q47759 |
| C | Low affinity penicillin-binding protein 5 (PBP5) | protein | 595 | 32% helix, 27% strand | Q47759 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 21 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1077 | 0.82 | 0.83 | 90 | empty |
| 2 | 899 | 0.81 | 0.83 | 70 | empty |
| 3 | 598 | 0.72 | 0.80 | 65 | empty |
| 4 | 518 | 0.72 | 0.80 | 53 | empty |
| 5 | 412 | 0.64 | 0.78 | 38 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2100 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 2079 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 6G0K · Crystal structure of Enterococcus faecium D63r Penicillin-Binding protein 5 (PBP5fm) · 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 Q47759
- Elsewhere: RCSB PDB 6G0K · PDBe 6G0K · UniProt Q47759
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