Research workbench
Complex structure of the pseudomonas aeruginosa rhamnosyltransferase earp with the acceptor elongation factor ef-P
Analyse Complex structure of the pseudomonas aeruginosa rhamnosyltransferase earp with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6J7M
- Type
- protein
- Length
- 1,111 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Earp; Elongation factor P
- UniProt
- Q9HZZ1, Q9HZZ2
- Ligands
- TYD
- Pockets
- 15 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Earp | protein | 377 | 41% helix, 18% strand | Q9HZZ1 |
| M | Elongation factor P | protein | 178 | 3% helix, 57% strand | Q9HZZ2 |
| N | Elongation factor P | protein | 179 | 6% helix, 54% strand | Q9HZZ2 |
Ligands and binding sites
- TYD · Thymidine-5'-diphosphate · ligand · 2 copies · chains A, C
- GOL · Glycerol · additive · 2 copies · chains A, M, C, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 223 | 0.84 | 0.96 | 42 | TYD, GOL |
| 2 | 217 | 0.83 | 0.96 | 41 | TYD, GOL |
| 3 | 60 | 0.74 | 0.99 | 18 | empty |
| 4 | 867 | 0.73 | 0.77 | 94 | empty |
| 5 | 59 | 0.72 | 0.98 | 17 | empty |
Interfaces
3 interfaces between chains.
- C–N · 1084 Ų buried · 21 hydrogen bonds · protein-protein
- A–M · 1082 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 610 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 6J7M · Complex structure of the Pseudomonas aeruginosa rhamnosyltransferase EarP with the… · the same entry in another collection · chain N against N, TM-score 1.00
- Q9HZZ1 · AlphaFold monomer V2.0 prediction for protein-arginine rhamnosyltransferase (Q9HZZ1) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q9HZZ2 · AlphaFold monomer V2.0 prediction for elongation factor P (Q9HZZ2) · a predicted model of the same protein · chain N against A, TM-score 0.69
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 Q9HZZ1
- Every structure of UniProt Q9HZZ2
- Elsewhere: RCSB PDB 6J7M · PDBe 6J7M · UniProt Q9HZZ1 · UniProt Q9HZZ2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.