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Structure of the periplasmic binding protein (pbp) melb (ATU4661) in complex with galactinol 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
- 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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