Research workbench
Atomic resolution structure of apo-form of rafe from streptococcus pneumoniae
Analyse Atomic resolution structure of apo-form of rafe from streptococcus pneumoniae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HEU
- Type
- protein
- Length
- 1,171 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sugar ABC transporter, sugar-binding protein
- UniProt
- Q97NW2
- Ligands
- NA, CL
- Pockets
- 18 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sugar ABC transporter, sugar-binding protein | protein | 391 | 46% helix, 14% strand | Q97NW2 |
| B, C | Sugar ABC transporter, sugar-binding protein | protein | 390 | 47% helix, 14% strand | Q97NW2 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, C
- CL · Chloride ion · ion · 3 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 171 | 0.60 | 0.83 | 24 | empty |
| 2 | 226 | 0.55 | 0.79 | 25 | empty |
| 3 | 213 | 0.55 | 0.78 | 25 | empty |
| 4 | 338 | 0.54 | 0.74 | 42 | empty |
| 5 | 280 | 0.52 | 0.75 | 33 | empty |
Interfaces
3 interfaces between chains.
- A–B · 573 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 461 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 456 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2HEU · Atomic resolution structure of apo-form of RafE from Streptococcus pneumoniae · the same entry in another collection · 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 Q97NW2
- Elsewhere: RCSB PDB 2HEU · PDBe 2HEU · UniProt Q97NW2
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