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Crystal structure of truncated bacteriophage hyaluronan lyase hylp in complex with unsaturated hyaluronan tetra-saccharides
Analyse Crystal structure of truncated bacteriophage hyaluronan lyase hylp in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WWX
- Type
- protein
- Length
- 816 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hyaluronoglucosaminidase
- EC
- 3.2.1.35
- UniProt
- P15316
- Ligands
- GCD, NAG, BDP, NI
- Pockets
- 4 · best druggability 0.28
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hyaluronoglucosaminidase (EC 3.2.1.35) | protein | 273 | 14% helix, 33% strand | P15316 |
| B | Hyaluronoglucosaminidase (EC 3.2.1.35) | protein | 271 | 14% helix, 33% strand | P15316 |
| C | Hyaluronoglucosaminidase (EC 3.2.1.35) | protein | 272 | 14% helix, 33% strand | P15316 |
Ligands and binding sites
- GCD · 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid · ligand · 6 copies · chains A, B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, C
- BDP · beta-D-glucopyranuronic acid · sugar · 6 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
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 59 | 0.28 | 0.74 | 17 | empty |
| 2 | 59 | 0.28 | 0.74 | 15 | empty |
| 3 | 60 | 0.28 | 0.74 | 16 | empty |
| 4 | 53 | 0.28 | 0.75 | 20 | BDP, NAG |
Interfaces
3 interfaces between chains.
- A–C · 9360 Ų buried · 209 hydrogen bonds · protein-protein
- A–B · 9296 Ų buried · 216 hydrogen bonds · protein-protein
- B–C · 9250 Ų buried · 219 hydrogen bonds · protein-protein
Compared structures
- 6WWX · Crystal structure of truncated bacteriophage hyaluronan lyase HylP in complex 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 6WWX · PDBe 6WWX · UniProt P15316
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