MolNFT v1 · #147865 · protein
Structure of the periplasmic binding protein (pbp) melb (ATU4661) in complex with stachyose from agrobacterium fabrum C58
6EQ1 · Periplasmic alpha-galactoside-binding protein: “Structure of the periplasmic binding protein (pbp) melb (ATU4661) in complex with stachyose from…”. X-ray diffraction, 5 ligands (TTV, ZCD, GLC), 13 pockets (best druggability 0.84).…
- PDB
- 6EQ1
- Type
- protein
- Length
- 1,340 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic alpha-galactoside-binding protein
- UniProt
- A0A083ZM57
- Ligands
- TTV, ZCD, GLC, GLA, CA
- Pockets
- 13 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Periplasmic alpha-galactoside-binding protein | protein | 671 | 30% helix, 19% strand | A0A083ZM57 |
| A | Periplasmic alpha-galactoside-binding protein | protein | 669 | 30% helix, 19% strand | A0A083ZM57 |
Ligands and binding sites
- TTV · Beta-D-psicofuranose · ligand · 2 copies · chains B, A
- ZCD · Alpha-D-idopyranose · ligand · 2 copies · chains B, A
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains B, A
- GLA · alpha-D-galactopyranose · sugar · 2 copies · chains B, A
- CA · Calcium ion · metal · 9 copies · chains B, A
- EDO · 1,2-ethanediol · additive · 13 copies · chains B, A
- PEG · Di(hydroxyethyl)ether · additive · 8 copies · chains B, A
- PG4 · Tetraethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 354 | 0.84 | 0.93 | 40 | TTV, GLC, ZCD, GLA |
| 2 | 679 | 0.82 | 0.86 | 72 | TTV, GLC, ZCD, GLA |
| 3 | 654 | 0.75 | 0.81 | 72 | empty |
| 4 | 52 | 0.70 | 0.99 | 24 | empty |
| 5 | 238 | 0.65 | 0.83 | 33 | empty |
Interfaces
1 interface between chains.
- B–A · 461 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6EQ1 · Structure of the periplasmic binding protein (PBP) MelB (Atu4661) in complex with… · the same entry in another collection · chain B against B, 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 A0A083ZM57
- Elsewhere: RCSB PDB 6EQ1 · PDBe 6EQ1 · UniProt A0A083ZM57
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