MolNFT v1 · #125208 · protein
Structure of cntnw in an inward-facing substrate-bound state
5L26 · Nucleoside permease: “Structure of cntnw in an inward-facing substrate-bound state”. X-ray diffraction, 3 ligands (6ZL, URI, NA), 20 pockets (best druggability 0.88). MolNFT v1 #125208 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5L26
- Type
- protein
- Length
- 1,240 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside permease
- UniProt
- G4CRQ5
- Ligands
- 6ZL, URI, NA
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleoside permease | protein | 419 | 76% helix, 0% strand | G4CRQ5 |
| B | Nucleoside permease | protein | 415 | 77% helix, 0% strand | G4CRQ5 |
| C | Nucleoside permease | protein | 406 | 76% 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 · 9 copies · chains A, C, B
- URI · Uridine · ligand · 3 copies · chains A, B, C
- NA · Sodium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 691 | 0.88 | 0.92 | 43 | empty |
| 2 | 541 | 0.73 | 0.81 | 51 | URI |
| 3 | 456 | 0.72 | 0.82 | 36 | URI |
| 4 | 531 | 0.72 | 0.81 | 54 | URI |
| 5 | 420 | 0.67 | 0.79 | 43 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1334 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 1320 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 1287 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5L26 · Structure of CNTnw in an inward-facing substrate-bound 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 5L26 · PDBe 5L26 · UniProt G4CRQ5
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