MolNFT v1 · #189080 · protein
Difructose dianhydride I SYNTHASE/HYDROLASE (ALPHAFFASE1) from bifidobacterium dentium, ligand-free form
7V1V: “Difructose dianhydride I SYNTHASE/HYDROLASE (ALPHAFFASE1) from bifidobacterium dentium, ligand-free form”. X-ray diffraction, 1 ligand (CA), 20 pockets (best druggability 0.78). MolNFT v1 #189080 on GenesisL1: 3D structure, binding…
- PDB
- 7V1V
- Type
- protein
- Length
- 2,678 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Difructose dianhydride I SYNTHASE/HYDROLASE (ALPHAFFASE1)
- UniProt
- A0A6L9SN29
- Ligands
- CA
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Difructose dianhydride I SYNTHASE/HYDROLASE (ALPHAFFASE1) | protein | 447 | 20% helix, 33% strand | A0A6L9SN29 |
| B, C, D, E | Difructose dianhydride I SYNTHASE/HYDROLASE (ALPHAFFASE1) | protein | 446 | 20% helix, 33% strand | A0A6L9SN29 |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains A, F, B, E, C, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains B, D, F
- TAR · D(-)-tartaric acid · additive · 2 copies · chains C, D, A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1060 | 0.78 | 0.80 | 117 | empty |
| 2 | 1181 | 0.77 | 0.79 | 121 | empty |
| 3 | 80 | 0.76 | 0.98 | 20 | empty |
| 4 | 81 | 0.75 | 0.98 | 21 | empty |
| 5 | 76 | 0.74 | 0.98 | 23 | empty |
Interfaces
12 interfaces between chains.
- A–F · 2977 Ų buried · 47 hydrogen bonds · protein-protein
- A–C · 2930 Ų buried · 45 hydrogen bonds · protein-protein
- D–E · 2887 Ų buried · 45 hydrogen bonds · protein-protein
- B–E · 2865 Ų buried · 45 hydrogen bonds · protein-protein
- B–D · 2849 Ų buried · 49 hydrogen bonds · protein-protein
Compared structures
- 7V1V · Difructose dianhydride I synthase/hydrolase (alphaFFase1) from Bifidobacterium dentium… · 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 A0A6L9SN29
- Elsewhere: RCSB PDB 7V1V · PDBe 7V1V · UniProt A0A6L9SN29
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