Research workbench
Crystal structure of hewl with HEXATUNGSTOTELLURATE(VI)
Analyse Crystal structure of hewl with HEXATUNGSTOTELLURATE(VI) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PHI
- Type
- protein
- Length
- 508 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysozyme C
- EC
- 3.2.1.17
- UniProt
- P00698
- Ligands
- TEW, NA
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Lysozyme C (EC 3.2.1.17) | protein | 127 | 43% helix, 11% strand | P00698 |
Ligands and binding sites
- TEW · 6-tungstotellurate(VI) · ligand · 8 copies · chains A, D, B, C
- NA · Sodium ion · metal · 6 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 2 copies · chains A, D
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 440 | 0.65 | 0.78 | 53 | ACT |
| 2 | 192 | 0.58 | 0.81 | 37 | NA |
| 3 | 264 | 0.57 | 0.77 | 38 | NA |
| 4 | 176 | 0.50 | 0.77 | 21 | empty |
Interfaces
6 interfaces between chains.
- A–D · 606 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 572 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 522 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 470 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 158 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 4PHI · Crystal structure of HEWL with hexatungstotellurate(VI) · the same entry in another collection · chain B against B, 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 P00698
- Elsewhere: RCSB PDB 4PHI · PDBe 4PHI · UniProt P00698
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