MolNFT v1 · #147862 · protein
Structure of the pbp melb (ATU4661) in complex with raffinose from A.FABRUM C58
6EPY · Periplasmic alpha-galactoside-binding protein: “Structure of the pbp melb (ATU4661) in complex with raffinose from A.FABRUM C58”. X-ray diffraction, 4 ligands (FRU, GLC, GLA), 20 pockets (best druggability 0.84). MolNFT v1 #147862…
- PDB
- 6EPY
- Type
- protein
- Length
- 2,672 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic alpha-galactoside-binding protein
- UniProt
- A0A083ZM57
- Ligands
- FRU, GLC, GLA, CA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Periplasmic alpha-galactoside-binding protein | protein | 669 | 31% helix, 19% strand | A0A083ZM57 |
| D | Periplasmic alpha-galactoside-binding protein | protein | 665 | 31% helix, 19% strand | A0A083ZM57 |
Ligands and binding sites
- FRU · beta-D-fructofuranose · sugar · 4 copies · chains A, B, C, D
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- GLA · alpha-D-galactopyranose · sugar · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 125 copies · chains A, D, B, C
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, C, 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 335 | 0.84 | 0.94 | 39 | FRU, GLC, GLA |
| 2 | 337 | 0.84 | 0.94 | 42 | FRU, GLC, GLA |
| 3 | 370 | 0.82 | 0.91 | 48 | FRU, GLC, GLA |
| 4 | 365 | 0.82 | 0.91 | 46 | FRU, GLC, GLA |
| 5 | 1096 | 0.76 | 0.78 | 91 | CA |
Interfaces
4 interfaces between chains.
- A–C · 738 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 640 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 434 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 21 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 56 modified, 4 disulfide (engineered, disulfide).
Compared structures
- 6EPY · Structure of the PBP MelB (Atu4661) in complex with raffinose from A.fabrum C58 · 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 6EPY · PDBe 6EPY · UniProt A0A083ZM57
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