Research workbench
Structure of cntnw N149L in the intermediate 1 state
Analyse Structure of cntnw N149L in the intermediate 1 state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5L27
- Type
- protein
- Length
- 1,212 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside permease
- UniProt
- G4CRQ5
- Ligands
- 6ZL
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleoside permease | protein | 415 | 73% helix, 0% strand | G4CRQ5 |
| B | Nucleoside permease | protein | 411 | 74% helix, 0% strand | G4CRQ5 |
| C | Nucleoside permease | protein | 386 | 71% helix, 0% strand | G4CRQ5 |
Ligands and binding sites
- 6ZL · 2-{[(4-O-alpha-D-glucopyranosyl-beta-D-glucopyranosyl) oxy]methyl}-2-octyldecyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 731 | 0.88 | 0.91 | 43 | empty |
| 2 | 586 | 0.81 | 0.86 | 51 | empty |
| 3 | 101 | 0.76 | 0.96 | 24 | empty |
| 4 | 512 | 0.75 | 0.83 | 48 | empty |
| 5 | 622 | 0.74 | 0.80 | 81 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1280 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 1240 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 1234 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5L27 · Structure of CNTnw N149L in the intermediate 1 state · 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 G4CRQ5
- Elsewhere: RCSB PDB 5L27 · PDBe 5L27 · UniProt G4CRQ5
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