MolNFT v1 · #125211 · protein
Structure of cntnw N149S, E332A in an outward-facing state
5L2B · Nucleoside permease: “Structure of cntnw N149S, E332A in an outward-facing state”. X-ray diffraction, 1 ligand (6ZL), 19 pockets (best druggability 0.88). MolNFT v1 #125211 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5L2B
- Type
- protein
- Length
- 1,239 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside permease
- UniProt
- G4CRQ5
- Ligands
- 6ZL
- Pockets
- 19 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleoside permease | protein | 421 | 72% helix, 0% strand | G4CRQ5 |
| B | Nucleoside permease | protein | 413 | 75% helix, 0% strand | G4CRQ5 |
| C | Nucleoside permease | protein | 405 | 70% 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 · 3 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 707 | 0.88 | 0.92 | 42 | empty |
| 2 | 598 | 0.73 | 0.80 | 50 | empty |
| 3 | 429 | 0.72 | 0.83 | 52 | empty |
| 4 | 491 | 0.72 | 0.81 | 48 | empty |
| 5 | 381 | 0.66 | 0.79 | 39 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1390 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 1294 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 1280 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5L2B · Structure of CNTnw N149S, E332A in an outward-facing 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 5L2B · PDBe 5L2B · UniProt G4CRQ5
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