Research workbench
Crystal structure of nzeb in complex with cyclo-(L-TRP-L-pro) and cyclo-(L-TRP-L-TRP)
Analyse Crystal structure of nzeb in complex with cyclo-(L-TRP-L-pro) and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XAK
- Type
- protein
- Length
- 794 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nzeb
- Ligands
- HEM, QRP, UYM
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nzeb | protein | 396 | 51% helix, 11% strand | — |
| B | Nzeb | protein | 398 | 51% helix, 11% strand | — |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- QRP · (3S,8aS)-3-(1H-indol-3-ylmethyl)hexahydropyrrolo[1,2-a]pyrazine-1,4-dione · ligand · 2 copies · chains A, B
- UYM · (3S,6S)-3,6-bis[(1H-indol-3-yl)methyl]piperazine-2,5-dione · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1001 | 0.86 | 0.86 | 84 | HEM, QRP, UYM |
| 2 | 997 | 0.85 | 0.86 | 86 | HEM, QRP, UYM |
| 3 | 328 | 0.65 | 0.80 | 43 | empty |
| 4 | 88 | 0.45 | 0.80 | 22 | empty |
| 5 | 145 | 0.43 | 0.76 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 546 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 6XAK · Crystal structure of NzeB in complex with cyclo-(L-Trp-L-Pro) and cyclo-(L-Trp-L-Trp) · 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 6XAK · PDBe 6XAK
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