Research workbench
The interaction of CHLORIDO(1,5-CYCLOOCTADIENE)([4-(2-((tert- BUTOXYCARBONYL)AMINO)-3-methoxy-3-oxopropyl)-1,3-dimethyl-1H- imidazol-3-IDE])RHODIUM(I) with hewl after 1 month
Analyse The interaction of CHLORIDO(1,5-CYCLOOCTADIENE)([4-(2-((tert… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WRM
- Type
- protein
- Length
- 129 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysozyme
- EC
- 3.2.1.17
- UniProt
- B8YK79
- Ligands
- U8G, NA, RH, CL
- Pockets
- 1 · best druggability 0.32
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysozyme (EC 3.2.1.17) | protein | 129 | 41% helix, 11% strand | B8YK79 |
Ligands and binding sites
- U8G · (4-{2-[(tert-butoxycarbonyl)amino]-3-methoxy-3-oxopropyl}-1,3-dimethyl-2,3-dihydro-1H-imidazol-2-yl) rhodium · ligand · chains A
- NA · Sodium ion · metal · chains A
- RH · Rhodium · metal · chains A
- CL · Chloride ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 71 | 0.32 | 0.75 | 16 | empty |
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6WRM · The interaction of chlorido(1,5-cyclooctadiene)([4-(2-((tert-butoxycarbonyl)amino)-3-metho… · 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 B8YK79
- Elsewhere: RCSB PDB 6WRM · PDBe 6WRM · UniProt B8YK79
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