MolNFT v1 · #138883 · protein
Earp bound with domain I of ef-P
5WXK: “Earp bound with domain I of ef-P”. X-ray diffraction, 3 ligands (TYD, NI, SO4), 5 pockets (best druggability 0.81). MolNFT v1 #138883 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5WXK
- Type
- protein
- Length
- 441 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Earp; Elongation factor P
- UniProt
- E6MVV9, E6MVW0
- Ligands
- TYD, NI, SO4
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Earp | protein | 375 | 43% helix, 18% strand | E6MVV9 |
| B | Elongation factor P | protein | 66 | 5% helix, 62% strand | E6MVW0 |
Ligands and binding sites
- TYD · Thymidine-5'-diphosphate · ligand · chains A
- NI · Nickel (II) ion · metal · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A
- BME · Beta-mercaptoethanol · additive · 3 copies · chains A
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 221 | 0.81 | 0.94 | 52 | TYD |
| 2 | 119 | 0.60 | 0.86 | 22 | BME |
| 3 | 98 | 0.41 | 0.77 | 22 | empty |
| 4 | 52 | 0.38 | 0.80 | 16 | empty |
| 5 | 68 | 0.33 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 941 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (additive adduct).
Compared structures
- 5WXK · EarP bound with domain I of EF-P · the same entry in another collection · chain A against A, TM-score 1.00
- E6MVV9 · AlphaFold monomer V2.0 prediction for protein-arginine rhamnosyltransferase (E6MVV9) · a predicted model of the same protein · chain A against A, TM-score 0.99
- E6MVW0 · AlphaFold monomer V2.0 prediction for elongation factor P (E6MVW0) · a predicted model of the same protein · chain B against A, TM-score 0.88
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 E6MVV9
- Every structure of UniProt E6MVW0
- Elsewhere: RCSB PDB 5WXK · PDBe 5WXK · UniProt E6MVV9 · UniProt E6MVW0
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