Research workbench
1YR-Y: lysozyme with re cluster 1 year on shelf
Analyse 1YR-Y: lysozyme with re cluster 1 year on shelf in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RO5
- Type
- protein
- Length
- 258 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysozyme C
- EC
- 3.2.1.17
- UniProt
- P00698
- Ligands
- QEB, RRE, RE, NA, CL
- Pockets
- 2 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lysozyme C (EC 3.2.1.17) | protein | 129 | 40% helix, 11% strand | P00698 |
Ligands and binding sites
- QEB · [Re4(mu3-OH)4(CO)12] · ligand · 6 copies · chains A
- RRE · fac-tricarbonyl-triaqua rhenium(I) · ligand · 2 copies · chains A, B
- RE · Rhenium · metal · 13 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 376 | 0.62 | 0.77 | 53 | CL, RE, ACT |
| 2 | 65 | 0.31 | 0.75 | 18 | ACT, RE |
Interfaces
1 interface between chains.
- A–B · 304 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6RO5 · 1Yr-Y: Lysozyme with Re Cluster 1 year on shelf · 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 P00698
- Elsewhere: RCSB PDB 6RO5 · PDBe 6RO5 · UniProt P00698
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