Research workbench
Crystal structure of nzeb in complex with cyclo-(L-TRP-L-val)
Analyse Crystal structure of nzeb in complex with cyclo-(L-TRP-L-val) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XAL
- Type
- protein
- Length
- 394 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nzeb
- Ligands
- UYG, HEM
- Pockets
- 2 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nzeb | protein | 394 | 51% helix, 11% strand | — |
Ligands and binding sites
- UYG · (3S,6S)-3-[(1H-indol-3-yl)methyl]-6-(propan-2-yl) piperazine-2,5-dione · ligand · 2 copies · chains A
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
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 | 1051 | 0.85 | 0.85 | 85 | HEM, UYG |
| 2 | 96 | 0.40 | 0.77 | 17 | empty |
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 6XAL · Crystal structure of NzeB in complex with cyclo-(L-Trp-L-Val) · 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
- Elsewhere: RCSB PDB 6XAL · PDBe 6XAL
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