MolNFT v1 · #187658 · protein
Chlorella virus hyaluronan synthase inhibited by udp
7SP7: “Chlorella virus hyaluronan synthase inhibited by udp”. Electron microscopy, 4 ligands (3PE, Y01, UDP), 8 pockets (best druggability 0.88). MolNFT v1 #187658 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7SP7
- Type
- protein
- Length
- 739 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hyaluronan synthase; Nanobody 872; Nanobody 881
- UniProt
- M1H2Q1
- Ligands
- 3PE, Y01, UDP, MN
- Pockets
- 8 · best druggability 0.88
Structure
electron microscopy · 3 distinct chains · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hyaluronan synthase | protein | 497 | 61% helix, 12% strand | M1H2Q1 |
| B | Nanobody 872 | protein | 124 | 5% helix, 47% strand | — |
| C | Nanobody 881 | protein | 118 | 0% helix, 42% strand | — |
Ligands and binding sites
- 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · chains A, B
- Y01 · Cholesterol hemisuccinate · ligand · chains A
- UDP · Uridine-5'-diphosphate · 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
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1019 | 0.88 | 0.89 | 89 | Y01, UDP, MN |
| 2 | 102 | 0.50 | 0.81 | 15 | empty |
| 3 | 157 | 0.43 | 0.75 | 28 | empty |
| 4 | 105 | 0.40 | 0.76 | 18 | empty |
| 5 | 96 | 0.36 | 0.75 | 19 | empty |
Interfaces
2 interfaces between chains.
- A–C · 843 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 636 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7SP7 · Chlorella virus hyaluronan synthase inhibited by UDP · 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 7SP7 · PDBe 7SP7 · UniProt M1H2Q1
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