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