MolNFT v1 · #147799 · protein
Physcomitrella patens bbe-like 1 variant D396N
6EO5 · Ppbbe-like 1 D396N: “Physcomitrella patens bbe-like 1 variant D396N”. X-ray diffraction, 2 ligands (FAD, NAG), 7 pockets (best druggability 0.84). MolNFT v1 #147799 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6EO5
- Type
- protein
- Length
- 925 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ppbbe-like 1 D396N
- Ligands
- FAD, NAG
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ppbbe-like 1 D396N | protein | 463 | 35% helix, 23% strand | — |
| B | Ppbbe-like 1 D396N | protein | 462 | 35% helix, 23% strand | — |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 592 | 0.84 | 0.89 | 71 | FAD |
| 2 | 652 | 0.83 | 0.87 | 77 | FAD |
| 3 | 347 | 0.66 | 0.80 | 28 | empty |
| 4 | 448 | 0.64 | 0.78 | 50 | empty |
| 5 | 354 | 0.60 | 0.77 | 45 | empty |
Interfaces
1 interface between chains.
- A–B · 1027 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor, 2 disulfide, 2 glycan (flavinylation, disulfide, N-glycosylation).
Compared structures
- 6EO5 · Physcomitrella patens BBE-like 1 variant D396N · 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 6EO5 · PDBe 6EO5
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