MolNFT v1 · #168990 · protein
Crystal structure of truncated streptococcal bacteriophage hyaluronidase complexed with unsaturated hyaluronan hexa-saccharides
6WXA · Hyaluronan lyase: “Crystal structure of truncated streptococcal bacteriophage hyaluronidase complexed with unsaturated…”. X-ray diffraction, 4 ligands (GCD, NAG, BDP), 2 pockets (best druggability 0.30). MolNFT v1 #168990 on…
- PDB
- 6WXA
- Type
- protein
- Length
- 825 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hyaluronan lyase
- EC
- 4.2.2.1
- UniProt
- P15316
- Ligands
- GCD, NAG, BDP, NI
- Pockets
- 2 · best druggability 0.30
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hyaluronan lyase (EC 4.2.2.1) | protein | 276 | 14% helix, 32% strand | P15316 |
| B | Hyaluronan lyase (EC 4.2.2.1) | protein | 275 | 16% helix, 32% strand | P15316 |
| C | Hyaluronan lyase (EC 4.2.2.1) | protein | 274 | 15% helix, 33% strand | P15316 |
Ligands and binding sites
- GCD · 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid · ligand · 4 copies · chains A, B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, B, C
- BDP · beta-D-glucopyranuronic acid · sugar · 8 copies · chains A, B, C
- NI · Nickel (II) ion · metal · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 63 | 0.30 | 0.75 | 19 | empty |
| 2 | 54 | 0.27 | 0.74 | 22 | NAG, BDP |
Interfaces
3 interfaces between chains.
- A–B · 9434 Ų buried · 213 hydrogen bonds · protein-protein
- A–C · 9421 Ų buried · 210 hydrogen bonds · protein-protein
- B–C · 9360 Ų buried · 219 hydrogen bonds · protein-protein
Compared structures
- 6WXA · Crystal structure of truncated Streptococcal bacteriophage hyaluronidase complexed with… · 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 6WXA · PDBe 6WXA · UniProt P15316
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