MolNFT v1 · #184160 · protein
Crystal structure of a GH31 family sulfoquinovosidase mutant D455N from agrobacterium tumefaciens in complex with sulfoquinovosyl glycerol (sqgro)
7OFX · Alpha-glucosidase yihq: “Crystal structure of a GH31 family sulfoquinovosidase mutant D455N from agrobacterium tumefaciens in complex…”. X-ray diffraction, 1 ligand (VCW), 12 pockets (best druggability 0.78). MolNFT v1 #184160 on…
- PDB
- 7OFX
- Type
- protein
- Length
- 2,650 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-glucosidase yihq
- EC
- 3.2.1.20
- UniProt
- A0A083ZKV2
- Ligands
- VCW
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 26% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-glucosidase yihq (EC 3.2.1.20) | protein | 661 | 25% helix, 30% strand | A0A083ZKV2 |
| C | Alpha-glucosidase yihq (EC 3.2.1.20) | protein | 661 | 25% helix, 29% strand | A0A083ZKV2 |
| D | Alpha-glucosidase yihq (EC 3.2.1.20) | protein | 663 | 26% helix, 29% strand | A0A083ZKV2 |
| B | Alpha-glucosidase yihq (EC 3.2.1.20) | protein | 665 | 26% helix, 30% strand | A0A083ZKV2 |
Ligands and binding sites
- VCW · [(2S,3S,4S,5R,6S)-6-[(2R)-2,3-bis(oxidanyl)propoxy]-3, 4,5-tris(oxidanyl)oxan-2-yl]methanesulfonic acid · ligand · 4 copies · chains A, C, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 328 | 0.78 | 0.88 | 39 | VCW |
| 2 | 1010 | 0.77 | 0.79 | 95 | empty |
| 3 | 287 | 0.76 | 0.89 | 38 | VCW |
| 4 | 1047 | 0.76 | 0.78 | 94 | empty |
| 5 | 274 | 0.76 | 0.89 | 38 | VCW |
Interfaces
3 interfaces between chains.
- A–B · 905 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 828 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 30 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7OFX · Crystal structure of a GH31 family sulfoquinovosidase mutant D455N from Agrobacterium… · 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 A0A083ZKV2
- Elsewhere: RCSB PDB 7OFX · PDBe 7OFX · UniProt A0A083ZKV2
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