MolNFT v1 · #183225 · protein
X-ray structure of a multidomain bbgiii from bifidobacterium bifidum
7NIT · Beta-galactosidase: “X-ray structure of a multidomain bbgiii from bifidobacterium bifidum”. X-ray diffraction, 2 ligands (CA, SO4), 20 pockets (best druggability 0.79). MolNFT v1 #183225 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7NIT
- Type
- protein
- Length
- 7,449 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-galactosidase
- EC
- 3.2.1.23
- UniProt
- A0A415C3Q2
- Ligands
- CA, SO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-galactosidase (EC 3.2.1.23) | protein | 1239 | 11% helix, 42% strand | A0A415C3Q2 |
| B, E | Beta-galactosidase (EC 3.2.1.23) | protein | 1235 | 11% helix, 42% strand | A0A415C3Q2 |
| C | Beta-galactosidase (EC 3.2.1.23) | protein | 1243 | 12% helix, 42% strand | A0A415C3Q2 |
| D | Beta-galactosidase (EC 3.2.1.23) | protein | 1253 | 11% helix, 42% strand | A0A415C3Q2 |
| F | Beta-galactosidase (EC 3.2.1.23) | protein | 1244 | 11% helix, 41% strand | A0A415C3Q2 |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 4 copies · chains A, C, D, F
- GOL · Glycerol · additive · 8 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 971 | 0.79 | 0.81 | 91 | empty |
| 2 | 1152 | 0.76 | 0.79 | 107 | empty |
| 3 | 1180 | 0.76 | 0.79 | 111 | empty |
| 4 | 59 | 0.74 | 0.99 | 21 | empty |
| 5 | 536 | 0.74 | 0.82 | 55 | empty |
Interfaces
4 interfaces between chains.
- B–C · 793 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 684 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 665 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 563 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7NIT · X-ray structure of a multidomain BbgIII from Bifidobacterium bifidum · 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 A0A415C3Q2
- Elsewhere: RCSB PDB 7NIT · PDBe 7NIT · UniProt A0A415C3Q2
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