MolNFT v1 · #169393 · protein
Crystal structure of nzeb in complex with cyclo-(L-TRP-L-pro)
6XAI: “Crystal structure of nzeb in complex with cyclo-(L-TRP-L-pro)”. X-ray diffraction, 2 ligands (QRP, HEM), 9 pockets (best druggability 0.85). MolNFT v1 #169393 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6XAI
- Type
- protein
- Length
- 798 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nzeb
- Ligands
- QRP, HEM
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nzeb | protein | 399 | 51% helix, 11% strand | — |
Ligands and binding sites
- QRP · (3S,8aS)-3-(1H-indol-3-ylmethyl)hexahydropyrrolo[1,2-a]pyrazine-1,4-dione · ligand · 4 copies · chains A, B
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 967 | 0.85 | 0.86 | 83 | HEM, QRP |
| 2 | 975 | 0.85 | 0.86 | 78 | HEM, QRP |
| 3 | 372 | 0.65 | 0.80 | 46 | empty |
| 4 | 104 | 0.51 | 0.82 | 21 | empty |
| 5 | 177 | 0.48 | 0.77 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 519 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 6XAI · Crystal structure of NzeB in complex with cyclo-(L-Trp-L-Pro) · 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 6XAI · PDBe 6XAI
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