MolNFT v1 · #98519 · protein
Identifying ligand binding hot spots in proteins using brominated fragments
4LBV · Elongation factor tu-a: “Identifying ligand binding hot spots in proteins using brominated fragments”. X-ray diffraction, 5 ligands (GNP, MG, SO4), 4 pockets (best druggability 0.56). MolNFT v1 #98519 on GenesisL1: 3D structure…
- PDB
- 4LBV
- Type
- protein
- Length
- 403 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Elongation factor tu-a
- UniProt
- P60338
- Ligands
- GNP, MG, SO4, NH4, CL
- Pockets
- 4 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Elongation factor tu-a | protein | 403 | 24% helix, 33% strand | P60338 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains A
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 8 copies · chains A
- NH4 · Ammonium ion · ion · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 306 | 0.56 | 0.76 | 32 | SO4 |
| 2 | 83 | 0.47 | 0.82 | 23 | GNP, MG |
| 3 | 161 | 0.46 | 0.76 | 27 | empty |
| 4 | 69 | 0.37 | 0.77 | 16 | empty |
Compared structures
- 4LBV · Identifying ligand binding hot spots in proteins using brominated fragments · the same entry in another collection · chain A against A, TM-score 1.00
- P60338 · AlphaFold monomer V2.0 prediction for elongation factor tu-a (P60338) · a predicted model of the same protein · 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 P60338
- Elsewhere: RCSB PDB 4LBV · PDBe 4LBV · UniProt P60338
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