MolNFT v1 · #174612 · protein
Crystal structure of a dinucleotide-binding protein (Y246A) of ABC transporter endogenously bound to uridylyl-3'-5'-phospho-guanosine (form II)
7C0Z · Sugar ABC transporter, periplasmic sugar-binding protein: “Crystal structure of a dinucleotide-binding protein (Y246A) of ABC transporter endogenously bound to…”. X-ray diffraction, 1 ligand (FGO), 3 pockets (best druggability…
- PDB
- 7C0Z
- Type
- protein
- Length
- 785 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sugar ABC transporter, periplasmic sugar-binding protein
- UniProt
- Q5SLB4
- Ligands
- FGO
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sugar ABC transporter, periplasmic sugar-binding protein | protein | 393 | 49% helix, 19% strand | Q5SLB4 |
| B | Sugar ABC transporter, periplasmic sugar-binding protein | protein | 392 | 51% helix, 19% strand | Q5SLB4 |
Ligands and binding sites
- FGO · [(1s,3r,3ar,6as)-3-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-5,5-bis(oxidanyl)-1,3,3A,4,6,6A-hexahydrocyclopenta[c]furan-1-yl]methyl [(2R,3S,4R, 5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-2-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl] hydrogen phosphate · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 505 | 0.73 | 0.82 | 59 | FGO |
| 2 | 554 | 0.73 | 0.81 | 53 | FGO |
| 3 | 630 | 0.68 | 0.77 | 56 | empty |
Interfaces
1 interface between chains.
- A–B · 347 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7C0Z · Crystal structure of a dinucleotide-binding protein (Y246A) of ABC transporter… · 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 Q5SLB4
- Elsewhere: RCSB PDB 7C0Z · PDBe 7C0Z · UniProt Q5SLB4
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