Research workbench
Structure of the periplasmic binding protein (pbp) melb (ATU4661) in complex with galactose from agrobacterium tumefacien 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
- 6EQ0
- Type
- protein
- Length
- 1,342 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic alpha-galactoside-binding protein
- UniProt
- A0A083ZM57
- Ligands
- GLA, CA, CL
- Pockets
- 14 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Periplasmic alpha-galactoside-binding protein | protein | 671 | 27% helix, 19% strand | A0A083ZM57 |
Ligands and binding sites
- GLA · alpha-D-galactopyranose · sugar · 2 copies · chains A, B
- CA · Calcium ion · metal · 17 copies · chains A, B
- CL · Chloride ion · ion · 16 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 21 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 332 | 0.84 | 0.94 | 39 | GLA, CA |
| 2 | 330 | 0.84 | 0.94 | 38 | GLA, CA |
| 3 | 941 | 0.79 | 0.81 | 91 | CA |
| 4 | 54 | 0.73 | 0.99 | 20 | empty |
| 5 | 254 | 0.61 | 0.80 | 33 | EDO, CL |
Interfaces
1 interface between chains.
- A–B · 458 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6EQ0 · Structure of the periplasmic binding protein (PBP) MelB (atu4661) in complex with… · 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 A0A083ZM57
- Elsewhere: RCSB PDB 6EQ0 · PDBe 6EQ0 · UniProt A0A083ZM57
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.