MolNFT v1 · #147863 · protein
Structure of the periplasmic binding protein melb (ATU4661) in complex with melibiose from agrobacterium fabrum C58
6EPZ · Periplasmic alpha-galactoside-binding protein: “Structure of the periplasmic binding protein melb (ATU4661) in complex with melibiose from agrobacterium…”. X-ray diffraction, 5 ligands (GLC, GLA, NA), 20 pockets (best druggability…
- PDB
- 6EPZ
- Type
- protein
- Length
- 2,687 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic alpha-galactoside-binding protein
- UniProt
- A0A083ZM57
- Ligands
- GLC, GLA, NA, MG, CL
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Periplasmic alpha-galactoside-binding protein | protein | 672 | 31% helix, 18% strand | A0A083ZM57 |
| D, B | Periplasmic alpha-galactoside-binding protein | protein | 671 | 31% helix, 19% strand | A0A083ZM57 |
| C | Periplasmic alpha-galactoside-binding protein | protein | 673 | 30% helix, 19% strand | A0A083ZM57 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, D, C, B
- GLA · alpha-D-galactopyranose · sugar · 4 copies · chains A, D, C, B
- NA · Sodium ion · metal · 28 copies · chains A, B, D, C
- MG · Magnesium ion · metal · 5 copies · chains A, D, C, B
- CL · Chloride ion · ion · chains D
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, D, C, B
- PEG · Di(hydroxyethyl)ether · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 378 | 0.83 | 0.92 | 46 | GLC, GLA |
| 2 | 460 | 0.81 | 0.89 | 60 | GLC, GLA |
| 3 | 338 | 0.81 | 0.91 | 45 | GLC, GLA |
| 4 | 450 | 0.81 | 0.89 | 59 | GLC, GLA, NA |
| 5 | 768 | 0.74 | 0.79 | 78 | empty |
Interfaces
4 interfaces between chains.
- A–C · 724 Ų buried · 7 hydrogen bonds · protein-protein
- D–B · 642 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 451 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 15 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6EPZ · Structure of the periplasmic binding protein MelB (Atu4661) in complex with melibiose… · 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 6EPZ · PDBe 6EPZ · UniProt A0A083ZM57
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