MolNFT v1 · #187659 · protein
Chlorella virus hyaluronan synthase bound to udp-glcnac
7SP8: “Chlorella virus hyaluronan synthase bound to udp-glcnac”. Electron microscopy, 4 ligands (UD1, 3PE, Y01), 9 pockets (best druggability 0.88). MolNFT v1 #187659 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7SP8
- Type
- protein
- Length
- 742 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hyaluronan synthase; Nanobody 872; Nanobody 881
- UniProt
- M1H2Q1
- Ligands
- UD1, 3PE, Y01, MN
- Pockets
- 9 · best druggability 0.88
Structure
electron microscopy · 3 distinct chains · 42% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hyaluronan synthase | protein | 500 | 61% helix, 13% strand | M1H2Q1 |
| B | Nanobody 872 | protein | 124 | 5% helix, 49% strand | — |
| C | Nanobody 881 | protein | 118 | 3% helix, 43% strand | — |
Ligands and binding sites
- UD1 · Uridine-diphosphate-N-acetylglucosamine · ligand · chains A
- 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · chains A, B
- Y01 · Cholesterol hemisuccinate · ligand · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1069 | 0.88 | 0.89 | 84 | UD1, Y01 |
| 2 | 108 | 0.56 | 0.84 | 16 | empty |
| 3 | 149 | 0.42 | 0.75 | 23 | empty |
| 4 | 86 | 0.37 | 0.77 | 15 | empty |
| 5 | 76 | 0.34 | 0.75 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–C · 838 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 654 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7SP8 · Chlorella virus Hyaluronan Synthase bound to UDP-GlcNAc · 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 M1H2Q1
- Elsewhere: RCSB PDB 7SP8 · PDBe 7SP8 · UniProt M1H2Q1
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