Research workbench
Structure of the periplasmic binding protein (pbp) melb (ATU4661) in complex with stachyose from agrobacterium fabrum C58
Analyse Structure of the periplasmic binding protein (pbp) melb (ATU4661) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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