MolNFT v1 · #187661 · protein
Chlorella virus hyaluronan synthase in the glcnac-primed, channel-open state
7SPA · Nanobody 872: “Chlorella virus hyaluronan synthase in the glcnac-primed, channel-open state”. Electron microscopy, 3 ligands (Y01, 3PE, NAG), 10 pockets (best druggability 0.87). MolNFT v1 #187661 on GenesisL1: 3D structure, binding…
- PDB
- 7SPA
- Type
- protein
- Length
- 737 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nanobody 872; Nanobody 881; Hyaluronan synthase
- UniProt
- M1H2Q1
- Ligands
- Y01, 3PE, NAG
- Pockets
- 10 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Nanobody 872 | protein | 123 | 7% helix, 51% strand | — |
| C | Nanobody 881 | protein | 117 | 3% helix, 36% strand | — |
| A | Hyaluronan synthase | protein | 497 | 61% helix, 12% strand | M1H2Q1 |
Ligands and binding sites
- Y01 · Cholesterol hemisuccinate · ligand · chains A
- 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · chains B, A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1064 | 0.87 | 0.88 | 96 | NAG, Y01 |
| 2 | 231 | 0.63 | 0.82 | 31 | empty |
| 3 | 127 | 0.56 | 0.83 | 32 | empty |
| 4 | 89 | 0.45 | 0.80 | 17 | empty |
| 5 | 89 | 0.39 | 0.77 | 14 | empty |
Interfaces
2 interfaces between chains.
- C–A · 861 Ų buried · 17 hydrogen bonds · protein-protein
- B–A · 589 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7SPA · Chlorella virus Hyaluronan Synthase in the GlcNAc-primed, channel-open state · the same entry in another collection · chain B against B, 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 M1H2Q1
- Elsewhere: RCSB PDB 7SPA · PDBe 7SPA · UniProt M1H2Q1
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