Research workbench
Crystal structure of streptococcal bacteriophage hyaluronidase: presence of a prokaryotic collagen and elucidation of catalytic mechanism
Analyse Crystal structure of streptococcal bacteriophage hyaluronidase: presence of a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WV2
- Type
- protein
- Length
- 815 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
- NI
- Pockets
- 3 · best druggability 0.32
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hyaluronan lyase (EC 4.2.2.1) | protein | 273 | 15% helix, 33% strand | P15316 |
| B, C | Hyaluronan lyase (EC 4.2.2.1) | protein | 271 | 15% helix, 33% strand | P15316 |
Ligands and binding sites
- 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
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 68 | 0.32 | 0.75 | 22 | empty |
| 2 | 64 | 0.32 | 0.76 | 19 | empty |
| 3 | 58 | 0.29 | 0.74 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–C · 9235 Ų buried · 211 hydrogen bonds · protein-protein
- A–B · 9223 Ų buried · 214 hydrogen bonds · protein-protein
- B–C · 9184 Ų buried · 216 hydrogen bonds · protein-protein
Compared structures
- 6WV2 · Crystal Structure of Streptococcal Bacteriophage Hyaluronidase: Presence of a Prokaryotic… · 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 6WV2 · PDBe 6WV2 · UniProt P15316
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