MolNFT v1 · #172057 · protein
Inward-open structure of human glycine transporter 1 in complex with a benzoylisoindoline inhibitor, sybody SB_GLYT1#7 and bound na and cl ions.
6ZPL · Sodium- and chloride-dependent glycine transporter 1: “Inward-open structure of human glycine transporter 1 in complex with a benzoylisoindoline inhibitor, sybody…”. X-ray diffraction, 3 ligands (QET, NA, CL), 17 pockets (best…
- PDB
- 6ZPL
- Type
- protein
- Length
- 1,561 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sodium- and chloride-dependent glycine transporter 1; Endoglucanase H; Sybody SB_GLYT1#7
- EC
- 3.2.1.4
- UniProt
- P48067, P16218
- Ligands
- QET, NA, CL
- Pockets
- 17 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 59% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Sodium- and chloride-dependent glycine transporter 1 | protein | 530 | 70% helix, 1% strand | P48067 |
| A | Sodium- and chloride-dependent glycine transporter 1 | protein | 518 | 73% helix, 1% strand | P48067 |
| C | Endoglucanase H (EC 3.2.1.4) | protein | 273 | 35% helix, 17% strand | P16218 |
| E, F | Sybody SB_GLYT1#7 | protein | 120 | 5% helix, 53% strand | — |
Ligands and binding sites
- QET · [5-fluoranyl-6-(oxan-4-yloxy)-1,3-dihydroisoindol-2-yl]-[5-methylsulfonyl-2-[2,2,3,3,3-pentakis(fluoranyl)propoxy]phenyl]methanone · ligand · 2 copies · chains B, A
- NA · Sodium ion · metal · 2 copies · chains B, A
- CL · Chloride ion · ion · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 549 | 0.75 | 0.82 | 53 | QET, NA |
| 2 | 712 | 0.75 | 0.80 | 66 | QET, NA |
| 3 | 447 | 0.67 | 0.79 | 37 | empty |
| 4 | 424 | 0.66 | 0.78 | 39 | empty |
| 5 | 157 | 0.58 | 0.82 | 26 | empty |
Interfaces
5 interfaces between chains.
- A–F · 847 Ų buried · 12 hydrogen bonds · protein-protein
- B–E · 840 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 110 Ų buried · 1 hydrogen bond · protein-protein
- B–A · 41 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 36 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6ZPL · Inward-open structure of human glycine transporter 1 in complex with a benzoylisoindoline… · the same entry in another collection · chain F against F, TM-score 1.00
- P16218 · AlphaFold monomer V2.0 prediction for endoglucanase H (P16218) · a predicted model of the same protein · chain C against A, TM-score 0.99
- P48067 · AlphaFold monomer V2.0 prediction for sodium- and chloride-dependent glycine transporter… · a predicted model of the same protein · chain B against A, TM-score 0.91
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 P48067
- Every structure of UniProt P16218
- Elsewhere: RCSB PDB 6ZPL · PDBe 6ZPL · UniProt P48067 · UniProt P16218
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