MolNFT v1 · #147872 · protein
Structure of the periplasmic binding protein (pbp) melb (ATU4661) in complex with galactinol from agrobacterium fabrum C58
6EQ8 · Periplasmic alpha-galactoside-binding protein: “Structure of the periplasmic binding protein (pbp) melb (ATU4661) in complex with galactinol from…”. X-ray diffraction, 4 ligands (BQZ, P4G, CA), 20 pockets (best druggability 0.84).…
- PDB
- 6EQ8
- Type
- protein
- Length
- 2,681 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic alpha-galactoside-binding protein
- UniProt
- A0A083ZM57
- Ligands
- BQZ, P4G, CA, CL
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, B, C | Periplasmic alpha-galactoside-binding protein | protein | 670 | 31% helix, 19% strand | A0A083ZM57 |
| A | Periplasmic alpha-galactoside-binding protein | protein | 671 | 30% helix, 19% strand | A0A083ZM57 |
Ligands and binding sites
- BQZ · galactinol · ligand · 4 copies · chains D, B, C, A
- P4G · 1-ethoxy-2-(2-ethoxyethoxy)ethane · ligand · 3 copies · chains D, C
- CA · Calcium ion · metal · 13 copies · chains D, B, C, A
- CL · Chloride ion · ion · 35 copies · chains D, B, C, A
- EDO · 1,2-ethanediol · additive · 39 copies · chains D, C, B, A
- PEG · Di(hydroxyethyl)ether · additive · 9 copies · chains D, B, C, A
- PG4 · Tetraethylene glycol · additive · 3 copies · chains D, C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 359 | 0.84 | 0.94 | 44 | EDO, BQZ |
| 2 | 381 | 0.84 | 0.93 | 47 | BQZ |
| 3 | 526 | 0.82 | 0.88 | 71 | BQZ, PEG, CL |
| 4 | 704 | 0.82 | 0.86 | 83 | EDO, BQZ, CA |
| 5 | 57 | 0.74 | 0.99 | 20 | empty |
Interfaces
3 interfaces between chains.
- D–C · 788 Ų buried · 7 hydrogen bonds · protein-protein
- B–A · 691 Ų buried · 7 hydrogen bonds · protein-protein
- D–A · 315 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6EQ8 · Structure of the periplasmic binding protein (PBP) MelB (Atu4661) in complex with… · the same entry in another collection · chain D against D, 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 6EQ8 · PDBe 6EQ8 · UniProt A0A083ZM57
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