MolNFT v1 · #56219 · protein
The galacto-N-biose-/lacto-N-biose I-binding protein (gl-bp) of the ABC transporter from bifidobacterium longum in complex with lacto-N- tetraose
2Z8F · Galacto-N-BIOSE/LACTO-N-biose I transporter substrate…: “The galacto-N-biose-/lacto-N-biose I-binding protein (gl-bp) of the ABC transporter from bifidobacterium…”. X-ray diffraction, 5 ligands (GAL, BGC, NAG), 8 pockets (best…
- PDB
- 2Z8F
- Type
- protein
- Length
- 800 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galacto-N-BIOSE/LACTO-N-biose I transporter substrate- binding protein
- UniProt
- A8W790
- Ligands
- GAL, BGC, NAG, ZN, NA
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Galacto-N-BIOSE/LACTO-N-biose I transporter substrate- binding protein | protein | 401 | 45% helix, 18% strand | A8W790 |
| B | Galacto-N-BIOSE/LACTO-N-biose I transporter substrate- binding protein | protein | 399 | 44% helix, 18% strand | A8W790 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- ZN · Zinc ion · metal · 5 copies · chains A, B
- NA · Sodium ion · metal · 3 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 467 | 0.71 | 0.81 | 47 | BGC, GAL, NAG |
| 2 | 406 | 0.69 | 0.81 | 41 | BGC, GAL, NAG |
| 3 | 240 | 0.68 | 0.85 | 31 | empty |
| 4 | 202 | 0.55 | 0.78 | 28 | empty |
| 5 | 174 | 0.53 | 0.79 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 459 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2Z8F · The galacto-N-biose-/lacto-N-biose I-binding protein (GL-BP) of the ABC transporter from… · 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 A8W790
- Elsewhere: RCSB PDB 2Z8F · PDBe 2Z8F · UniProt A8W790
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