MolNFT v1 · #149707 · protein
Crystal structure of enterococcus faecium D63R penicillin-binding protein 5 (PBP5FM)
6G88 · Low affinity penicillin-binding protein 5 (PBP5): “Crystal structure of enterococcus faecium D63R penicillin-binding protein 5 (PBP5FM)”. X-ray diffraction, 2 ligands (RB6, SO4), 16 pockets (best druggability 0.83). MolNFT v1…
- PDB
- 6G88
- Type
- protein
- Length
- 1,799 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
- RB6, SO4
- Pockets
- 16 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Low affinity penicillin-binding protein 5 (PBP5) | protein | 622 | 34% helix, 25% strand | Q47759 |
| B | Low affinity penicillin-binding protein 5 (PBP5) | protein | 580 | 32% helix, 25% strand | Q47759 |
| C | Low affinity penicillin-binding protein 5 (PBP5) | protein | 597 | 33% helix, 26% strand | Q47759 |
Ligands and binding sites
- RB6 · (2R)-2-[(1R)-1-{[(2Z)-2-(5-amino-1,2,4-thiadiazol-3-yl)-2-(hydroxyimino)acetyl]amino}-2-oxoethyl]-5-({2-oxo-1-[(3R)-pyr rolidin-3-yl]-2,5-dihydro-1H-pyrrol-3-yl}methyl)-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 913 | 0.83 | 0.85 | 96 | empty |
| 2 | 824 | 0.80 | 0.83 | 71 | empty |
| 3 | 1059 | 0.76 | 0.78 | 103 | SO4 |
| 4 | 596 | 0.72 | 0.80 | 65 | empty |
| 5 | 496 | 0.65 | 0.77 | 56 | RB6 |
Interfaces
2 interfaces between chains.
- A–B · 2127 Ų buried · 39 hydrogen bonds · protein-protein
- A–C · 2036 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 6G88 · Crystal structure of Enterococcus Faecium D63r Penicillin-Binding protein 5 (PBP5fm) · the same entry in another collection · chain B against B, 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 6G88 · PDBe 6G88 · UniProt Q47759
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.