MolNFT v1 · #136771 · protein
Crystal structure of fosfomycin resistance protein from klebsiella pneumoniae with bound fosfomycin
5V3D: “Crystal structure of fosfomycin resistance protein from klebsiella pneumoniae with bound fosfomycin”. X-ray diffraction, 3 ligands (FCN, MN, K), 4 pockets (best druggability 0.73). MolNFT v1 #136771 on GenesisL1: 3D structure…
- PDB
- 5V3D
- Type
- protein
- Length
- 275 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fosfomycin resistance protein
- UniProt
- W8UNW6
- Ligands
- FCN, MN, K
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fosfomycin resistance protein | protein | 138 | 27% helix, 36% strand | W8UNW6 |
| B | Fosfomycin resistance protein | protein | 137 | 27% helix, 35% strand | W8UNW6 |
Ligands and binding sites
- FCN · Fosfomycin · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
- EDO · 1,2-ethanediol · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 310 | 0.73 | 0.86 | 24 | empty |
| 2 | 122 | 0.53 | 0.82 | 22 | MN, FCN |
| 3 | 127 | 0.49 | 0.80 | 19 | MN, FCN, PEG |
| 4 | 75 | 0.36 | 0.77 | 13 | EDO |
Interfaces
1 interface between chains.
- A–B · 2727 Ų buried · 50 hydrogen bonds · protein-protein
Compared structures
- 5V3D · Crystal structure of fosfomycin resistance protein from Klebsiella pneumoniae with bound… · 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 W8UNW6
- Elsewhere: RCSB PDB 5V3D · PDBe 5V3D · UniProt W8UNW6
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