MolNFT v1 · #121787 · protein
Crystal structure of a marine metagenome trap solute binding protein specific for aromatic acid ligands (sorcerer II global ocean sampling expedition, unidentified microbe, locus tag GOS_1523157) in complex with co-purified 4-hydroxybenzoate
5I5P · Trap transporter solute binding protein: “Crystal structure of a marine metagenome trap solute binding protein specific for aromatic acid ligands…”. X-ray diffraction, 2 ligands (PHB, BR), 7 pockets (best druggability 0.71). MolNFT…
- PDB
- 5I5P
- Type
- protein
- Length
- 639 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trap transporter solute binding protein
- Ligands
- PHB, BR
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trap transporter solute binding protein | protein | 319 | 51% helix, 18% strand | — |
| B | Trap transporter solute binding protein | protein | 320 | 52% helix, 18% strand | — |
Ligands and binding sites
- PHB · P-hydroxybenzoic acid · ligand · 2 copies · chains A, B
- BR · Bromide ion · ion · 6 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.71 | 0.99 | 21 | PHB |
| 2 | 226 | 0.61 | 0.81 | 42 | PEG |
| 3 | 207 | 0.61 | 0.82 | 27 | empty |
| 4 | 240 | 0.58 | 0.79 | 31 | empty |
| 5 | 121 | 0.39 | 0.74 | 16 | BR |
Interfaces
1 interface between chains.
- A–B · 500 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 modified (engineered).
Compared structures
- 5I5P · Crystal structure of a marine metagenome TRAP solute binding protein specific for… · 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
- Elsewhere: RCSB PDB 5I5P · PDBe 5I5P
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