Research workbench
Earp bound with dtdp-rhamnose (co-crystal)
Analyse Earp bound with dtdp-rhamnose (co-crystal) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XVR
- Type
- protein
- Length
- 757 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Earp
- UniProt
- E6MVV9
- Ligands
- TRH, SO4
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Earp | protein | 381 | 42% helix, 19% strand | E6MVV9 |
| B | Earp | protein | 376 | 41% helix, 19% strand | E6MVV9 |
Ligands and binding sites
- TRH · 2'-deoxy-thymidine-beta-L-rhamnose · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 561 | 0.83 | 0.88 | 75 | TRH |
| 2 | 481 | 0.82 | 0.89 | 56 | TRH |
| 3 | 170 | 0.53 | 0.79 | 25 | empty |
| 4 | 68 | 0.47 | 0.83 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1007 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
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
- Elsewhere: RCSB PDB 5XVR · PDBe 5XVR · UniProt E6MVV9
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