MolNFT v1 · #169186 · protein
Crystal structure of full-length streptococcal bacteriophage hyaluronidase in complex with unsaturated hyaluronan octa-saccharides
6X3M · Hyaluronoglucosaminidase: “Crystal structure of full-length streptococcal bacteriophage hyaluronidase in complex with unsaturated…”. X-ray diffraction, 3 ligands (GCD, NAG, BDP), 13 pockets (best druggability 0.74). MolNFT v1…
- PDB
- 6X3M
- Type
- protein
- Length
- 3,241 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hyaluronoglucosaminidase
- EC
- 4.2.2.1
- UniProt
- P15316
- Ligands
- GCD, NAG, BDP
- Pockets
- 13 · best druggability 0.74
Structure
x-ray diffraction · 9 distinct chains · 11% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hyaluronoglucosaminidase (EC 4.2.2.1) | protein | 361 | 11% helix, 28% strand | P15316 |
| B | Hyaluronoglucosaminidase (EC 4.2.2.1) | protein | 361 | 12% helix, 27% strand | P15316 |
| C | Hyaluronoglucosaminidase (EC 4.2.2.1) | protein | 361 | 10% helix, 27% strand | P15316 |
| D | Hyaluronoglucosaminidase (EC 4.2.2.1) | protein | 349 | 9% helix, 27% strand | P15316 |
| E | Hyaluronoglucosaminidase (EC 4.2.2.1) | protein | 357 | 10% helix, 27% strand | P15316 |
| F | Hyaluronoglucosaminidase (EC 4.2.2.1) | protein | 366 | 11% helix, 26% strand | P15316 |
| G | Hyaluronoglucosaminidase (EC 4.2.2.1) | protein | 363 | 12% helix, 26% strand | P15316 |
| H | Hyaluronoglucosaminidase (EC 4.2.2.1) | protein | 361 | 13% helix, 26% strand | P15316 |
| I | Hyaluronoglucosaminidase (EC 4.2.2.1) | protein | 362 | 10% helix, 27% strand | P15316 |
Ligands and binding sites
- GCD · 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid · ligand · 18 copies · chains A, B, C, D, F, E, G, H, I
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 54 copies · chains A, C, B, D, E, F, G, H, I
- BDP · beta-D-glucopyranuronic acid · sugar · 36 copies · chains A, B, C, D, E, F, G, H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 60 | 0.74 | 0.99 | 22 | empty |
| 2 | 520 | 0.62 | 0.75 | 57 | empty |
| 3 | 170 | 0.54 | 0.79 | 25 | empty |
| 4 | 115 | 0.46 | 0.79 | 25 | empty |
| 5 | 107 | 0.46 | 0.79 | 23 | empty |
Interfaces
17 interfaces between chains.
- G–H · 11155 Ų buried · 208 hydrogen bonds · protein-protein
- E–F · 11105 Ų buried · 206 hydrogen bonds · protein-protein
- H–I · 11055 Ų buried · 201 hydrogen bonds · protein-protein
- A–B · 11001 Ų buried · 225 hydrogen bonds · protein-protein
- D–E · 10995 Ų buried · 217 hydrogen bonds · protein-protein
Compared structures
- 6X3M · Crystal structure of full-length Streptococcal bacteriophage hyaluronidase in complex… · 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 P15316
- Elsewhere: RCSB PDB 6X3M · PDBe 6X3M · UniProt P15316
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