MolNFT v1 · #129355 · protein
A GH31 family sulfoquinovosidase mutant D455N in complex with pnpsq
5OHS · Alpha-glucosidase yihq: “A GH31 family sulfoquinovosidase mutant D455N in complex with pnpsq”. X-ray diffraction, 4 ligands (NSQ, K, SCN), 20 pockets (best druggability 0.81). MolNFT v1 #129355 on GenesisL1: 3D structure, binding…
- PDB
- 5OHS
- Type
- protein
- Length
- 5,294 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-glucosidase yihq
- EC
- 3.2.1.20
- UniProt
- A0A083ZKV2
- Ligands
- NSQ, K, SCN, CL
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, H | Alpha-glucosidase yihq (EC 3.2.1.20) | protein | 661 | 26% helix, 30% strand | A0A083ZKV2 |
| B | Alpha-glucosidase yihq (EC 3.2.1.20) | protein | 663 | 26% helix, 29% strand | A0A083ZKV2 |
| D | Alpha-glucosidase yihq (EC 3.2.1.20) | protein | 662 | 26% helix, 29% strand | A0A083ZKV2 |
| F | Alpha-glucosidase yihq (EC 3.2.1.20) | protein | 664 | 27% helix, 29% strand | A0A083ZKV2 |
Ligands and binding sites
- NSQ · 4-nitrophenyl alpha-D-6-sulfoquinovoside · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- K · Potassium ion · metal · 2 copies · chains C, D
- SCN · Thiocyanate ion · ion · 8 copies · chains A, D, E, F, G, H
- CL · Chloride ion · ion · 6 copies · chains A, B, E, F, G, H
- EDO · 1,2-ethanediol · additive · 18 copies · chains A, B, C, D, E, F, G, H
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 9 copies · chains A, B, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 514 | 0.81 | 0.87 | 40 | NSQ |
| 2 | 520 | 0.80 | 0.87 | 42 | NSQ |
| 3 | 318 | 0.77 | 0.88 | 38 | EDO, NSQ |
| 4 | 307 | 0.77 | 0.89 | 39 | MPD, EDO, NSQ |
| 5 | 304 | 0.77 | 0.89 | 40 | EDO, NSQ |
Interfaces
8 interfaces between chains.
- C–E · 997 Ų buried · 19 hydrogen bonds · protein-protein
- D–F · 994 Ų buried · 19 hydrogen bonds · protein-protein
- B–H · 984 Ų buried · 18 hydrogen bonds · protein-protein
- A–G · 980 Ų buried · 18 hydrogen bonds · protein-protein
- A–H · 285 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5OHS · A GH31 family sulfoquinovosidase mutant D455N in complex with pNPSQ · the same entry in another collection · chain G against G, 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 A0A083ZKV2
- Elsewhere: RCSB PDB 5OHS · PDBe 5OHS · UniProt A0A083ZKV2
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