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Crystal structure of mannohexaose bound oligopeptide ABC transporter, periplasmic oligopeptide-binding protein (TM1223) from thermotoga maritima at 1.5 a resolution
Analyse Crystal structure of mannohexaose bound oligopeptide ABC transporter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PFY
- Type
- protein
- Length
- 1,076 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ABC transporter substrate-binding protein
- UniProt
- Q9X0V0
- Ligands
- BMA, MG, NO3
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ABC transporter substrate-binding protein | protein | 539 | 33% helix, 19% strand | Q9X0V0 |
| B | ABC transporter substrate-binding protein | protein | 537 | 33% helix, 20% strand | Q9X0V0 |
Ligands and binding sites
- BMA · beta-D-mannopyranose · sugar · 12 copies · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B
- NO3 · Nitrate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 977 | 0.86 | 0.87 | 78 | BMA |
| 2 | 1182 | 0.84 | 0.85 | 87 | BMA |
| 3 | 395 | 0.67 | 0.80 | 43 | NO3 |
| 4 | 149 | 0.54 | 0.81 | 31 | empty |
| 5 | 171 | 0.54 | 0.79 | 40 | empty |
Interfaces
1 interface between chains.
- A–B · 627 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4PFY · Crystal structure of mannohexaose bound oligopeptide ABC transporter, periplasmic… · 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 Q9X0V0
- Elsewhere: RCSB PDB 4PFY · PDBe 4PFY · UniProt Q9X0V0
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