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Crystal structure of mannobiose bound oligopeptide ABC transporter, periplasmic oligopeptide-binding protein (TM1226) from thermotoga maritima at 2.05 a resolution
Analyse Crystal structure of mannobiose bound oligopeptide ABC transporter, periplasmic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PFU
- Type
- protein
- Length
- 1,082 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ABC transporter substrate-binding protein
- UniProt
- G4FEC0
- Ligands
- BMA, MG, SO4
- Pockets
- 9 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ABC transporter substrate-binding protein | protein | 540 | 34% helix, 20% strand | G4FEC0 |
| B | ABC transporter substrate-binding protein | protein | 542 | 34% helix, 20% strand | G4FEC0 |
Ligands and binding sites
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 20 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 | 1118 | 0.87 | 0.88 | 96 | SO4 |
| 2 | 1177 | 0.86 | 0.87 | 93 | BMA, SO4 |
| 3 | 1154 | 0.86 | 0.87 | 95 | BMA, SO4 |
| 4 | 210 | 0.65 | 0.84 | 36 | empty |
| 5 | 78 | 0.56 | 0.87 | 17 | SO4 |
Interfaces
1 interface between chains.
- A–B · 1211 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4PFU · Crystal structure of mannobiose 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 G4FEC0
- Elsewhere: RCSB PDB 4PFU · PDBe 4PFU · UniProt G4FEC0
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