Research workbench
Crystal structure of solute-binding protein from enterococcus faecium with bound glutamate
Analyse Crystal structure of solute-binding protein from enterococcus faecium with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EYF
- Type
- protein
- Length
- 484 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate ABC superfamily ATP binding cassette transporter, binding protein
- UniProt
- Q3XZW5
- Ligands
- GGL, MG, CL
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate ABC superfamily ATP binding cassette transporter, binding protein | protein | 241 | 36% helix, 26% strand | Q3XZW5 |
| B | Glutamate ABC superfamily ATP binding cassette transporter, binding protein | protein | 243 | 35% helix, 26% strand | Q3XZW5 |
Ligands and binding sites
- GGL · Gamma-L-glutamic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 726 | 0.72 | 0.78 | 64 | CL |
| 2 | 251 | 0.65 | 0.82 | 28 | empty |
| 3 | 224 | 0.61 | 0.81 | 29 | empty |
| 4 | 130 | 0.53 | 0.82 | 28 | GGL |
| 5 | 127 | 0.40 | 0.75 | 24 | MG |
Interfaces
1 interface between chains.
- A–B · 1051 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 5EYF · Crystal Structure of Solute-binding Protein from Enterococcus faecium with Bound Glutamate · the same entry in another collection · chain B against B, 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 Q3XZW5
- Elsewhere: RCSB PDB 5EYF · PDBe 5EYF · UniProt Q3XZW5
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