MolNFT v1 · #189682 · protein
GH2 beta-galacturonate aqgala in complex with galacturonide
7VQM: “GH2 beta-galacturonate aqgala in complex with galacturonide”. X-ray diffraction, 2 ligands (GTR, CL), 20 pockets (best druggability 0.86). MolNFT v1 #189682 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7VQM
- Type
- protein
- Length
- 2,336 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GH2 beta-galacturonate aqgala
- Ligands
- GTR, CL
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | GH2 beta-galacturonate aqgala | protein | 584 | 20% helix, 34% strand | — |
Ligands and binding sites
- GTR · beta-D-galactopyranuronic acid · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 688 | 0.86 | 0.90 | 119 | empty |
| 2 | 593 | 0.84 | 0.90 | 107 | empty |
| 3 | 51 | 0.70 | 0.98 | 21 | empty |
| 4 | 334 | 0.67 | 0.81 | 35 | GTR |
| 5 | 318 | 0.67 | 0.82 | 34 | GTR |
Interfaces
6 interfaces between chains.
- C–D · 2842 Ų buried · 45 hydrogen bonds · protein-protein
- A–B · 2823 Ų buried · 48 hydrogen bonds · protein-protein
- A–D · 1187 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1180 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 63 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7VQM · GH2 beta-galacturonate AqGalA in complex with galacturonide · 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
- Elsewhere: RCSB PDB 7VQM · PDBe 7VQM
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