MolNFT v1 · #178088 · protein
Cryo-EM structure of rhizobium etli mprf
7F47 · Hypothetical conserved protein: “Cryo-EM structure of rhizobium etli mprf”. Electron microscopy, 2 ligands (PGW, 1K1), 14 pockets (best druggability 0.84). MolNFT v1 #178088 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7F47
- Type
- protein
- Length
- 830 residues
- Chains
- 1
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical conserved protein
- UniProt
- Q2K4J4
- Ligands
- PGW, 1K1
- Pockets
- 14 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 64% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical conserved protein | protein | 830 | 64% helix, 11% strand | Q2K4J4 |
Ligands and binding sites
- PGW · (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate · ligand · chains A
- 1K1 · [(2R)-1-[[(2R)-3-[(2S)-2,6-bis(azanyl)hexanoyl]oxy-2-oxidanyl-propoxy]-oxidanyl-phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (E)-octadec-9-enoate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1014 | 0.84 | 0.85 | 100 | 1K1 |
| 2 | 912 | 0.82 | 0.84 | 63 | PGW |
| 3 | 168 | 0.80 | 0.95 | 31 | empty |
| 4 | 103 | 0.62 | 0.87 | 18 | empty |
| 5 | 165 | 0.46 | 0.76 | 25 | empty |
Compared structures
- 7F47 · Cryo-EM structure of Rhizobium etli MprF · 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 Q2K4J4
- Elsewhere: RCSB PDB 7F47 · PDBe 7F47 · UniProt Q2K4J4
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